From 24784bef0b5eeb3eeed9ea72426312de825298b9 Mon Sep 17 00:00:00 2001 From: Vishal N Koparde Date: Tue, 12 Jun 2018 15:14:44 -0400 Subject: [PATCH] Skylers changes for centos7 / RNASeq --- Results-template/Scripts/Deseq2Report.Rmd | 27 +++- Results-template/Scripts/EdgerReport.Rmd | 27 +++- Results-template/Scripts/PcaReport.Rmd | 115 +++++++++++---- Results-template/Scripts/avia.pl | 6 +- Results-template/Scripts/genejunctioncounts.R | 7 +- Results-template/Scripts/karyoplot.py | 98 +++++++++---- Results-template/Scripts/maftools.R | 4 +- .../Scripts/make_sample_network.pl | 8 +- Rules/CAPmirseq-plus.snakefile | 2 +- Rules/InitialChIPseqQC.snakefile | 6 +- Rules/admixture_germline.rl | 2 +- Rules/admixture_somatic.rl | 2 +- Rules/admixture_wgs.rl | 2 +- Rules/admixture_wgs_somatic.rl | 2 +- Rules/all-exomeseq-germline.rl | 2 +- Rules/all-exomeseq-somatic-tumoronly.rl | 6 +- Rules/all-exomeseq-somatic.rl | 6 +- Rules/all-initialqc.rl | 4 +- Rules/all-rnafusion.rl | 6 +- Rules/all-rnaseqvar-somatic.rl | 2 +- Rules/all-rnaseqvargerm.rl | 2 +- Rules/all-wgs-somatic-tumoronly.rl | 6 +- Rules/all-wgs-somatic.rl | 6 +- Rules/all-wgslow.rl | 6 +- Rules/avia.rl | 2 +- Rules/bwa.mem.rl | 2 +- Rules/canvas_wgs_germ.rl | 2 +- Rules/canvas_wgs_somatic.rl | 2 +- Rules/canvas_wgs_tumoronly.rl | 2 +- Rules/cnvkit_germ.rl | 2 +- Rules/cnvkit_somatic.rl | 2 +- Rules/cnvkit_somatic_tumoronly.rl | 2 +- Rules/cnvkit_summary.rl | 2 +- Rules/cnvkit_summary_tumoronly.rl | 2 +- Rules/cnvkit_wgs_somatic.rl | 2 +- Rules/database_germline.rl | 2 +- Rules/database_somatic.rl | 2 +- Rules/database_somatic_tumoronly.rl | 2 +- Rules/fusioncatcher.rl | 2 +- Rules/fusioninsp_fuscatch.rl | 2 +- Rules/fusioninsp_starfus.rl | 2 +- Rules/gatk.haplotype.caller.rl | 2 +- Rules/gatk.merge.mutect2.chrom.rl | 12 +- Rules/gatk.merge.mutect2.chrom.tumoronly.rl | 12 +- Rules/gatk.merge.wgs.mutect2.chrom.rl | 8 +- .../gatk.merge.wgs.mutect2.chrom.tumoronly.rl | 12 +- Rules/gatk.mutect2.rl | 138 +++++++++--------- Rules/gatk.mutect2.tumoronly.rl | 138 +++++++++--------- Rules/gatk.realign.2.rl | 4 +- Rules/gatk.realign.2.rl.bak | 4 +- Rules/gatk.realign.rl | 2 +- Rules/gatk.recal.rl | 2 +- Rules/gatk_select_variants.rl | 2 +- Rules/initialqcrnaseq.snakefile | 19 ++- Rules/maftools.rl | 2 +- Rules/maftools_tumoronly.rl | 2 +- Rules/make_target_files.rl | 2 +- Rules/manta_somatic.rl | 2 +- Rules/manta_somatic_tumoronly.rl | 2 +- Rules/manta_wgs_somatic.rl | 2 +- Rules/manta_wgs_somatic_tumoronly.rl | 2 +- Rules/multiqc.rl | 2 +- Rules/multiqc_genomeseq.rl | 2 +- Rules/mutect.rl | 4 +- Rules/novocraft.novoalign.rl | 4 +- Rules/novocraft.novoalign.rl.bak | 4 +- Rules/novocraft.novoalign.rl~ | 4 +- Rules/novocraft.sort.rl | 2 +- Rules/novocraft.sort.rl.bak | 2 +- Rules/novocraft.sort.rl~ | 2 +- Rules/oncotator.rl | 2 +- Rules/oncotator_mutect.rl | 4 +- Rules/oncotator_mutect2.rl | 2 +- Rules/oncotator_strelka.rl | 2 +- Rules/qualimap.rl | 2 +- Rules/qualimap_wgs.rl | 2 +- Rules/rnaseq.snakefile | 3 +- Rules/rnaseqforfusions.rl | 16 +- Rules/scrnaseq.snakefile | 6 +- Rules/snpeff.rl | 2 +- Rules/strelka.rl | 4 +- Rules/theta.rl | 2 +- Rules/vcf2maf.rl | 6 +- Rules/vcf2maf_tumoronly.rl | 2 +- Rules/wgs_strelka.rl | 4 +- hg19.json | 8 +- hg38.json | 8 +- mm10.json | 8 +- pipeline_ctrl.sh | 2 +- pipeliner.py | 4 +- rules.json | 2 +- slurm.template | 2 +- standard-bin.json | 45 +++--- submit_slurm.template | 1 + 94 files changed, 540 insertions(+), 382 deletions(-) mode change 100755 => 100644 Rules/initialqcrnaseq.snakefile mode change 100755 => 100644 standard-bin.json diff --git a/Results-template/Scripts/Deseq2Report.Rmd b/Results-template/Scripts/Deseq2Report.Rmd index 18daa7a..b2ffeba 100755 --- a/Results-template/Scripts/Deseq2Report.Rmd +++ b/Results-template/Scripts/Deseq2Report.Rmd @@ -1,3 +1,4 @@ + --- title: "DESeq2 results" author: "CCBR RNAseq pipeline" @@ -143,12 +144,32 @@ Phenotype=sampleinfo$condition cell_rep=sampleinfo$label tedf1$group = as.factor(Phenotype) +pc1 = round(pca$sdev[1]^2/sum(pca$sdev^2)*100,2) +pc2 = round(pca$sdev[2]^2/sum(pca$sdev^2)*100,2) +pc3 = round(pca$sdev[3]^2/sum(pca$sdev^2)*100,2) + +pcafactor = as.factor(sampleinfo$condition) + +library(RColorBrewer) + +col <- brewer.pal(nlevels(pcafactor), "Paired") + +p <- plot_ly(as.data.frame(pca$x[,1:3]), x = ~PC1, y = ~PC2, z = ~PC3, color = pcafactor, colors = col, hoverinfo="text", + hovertext = ~sampleinfo$label) %>% + add_markers() %>% + layout(title = "PCA plot", + scene = list(xaxis = list(title = paste0("PC1 (",pc1,"%)")), + yaxis = list(title = paste0("PC2 (",pc2,"%)")), + zaxis = list(title = paste0("PC3 (",pc3,"%)")))) + +p + # plot(pca,type="lines") #Decide how many PC's are relevant for plotting #pca$x[,1:3] #look at first 3 PC's -plot3d(pca$x[,1:3],col = as.integer(tedf1$group),type="s",size=2) -group.v<-as.vector(cell_rep) -text3d(pca$x, pca$y, pca$z, group.v, cex=1.0, adj = 1.2) +#plot3d(pca$x[,1:3],col = as.integer(tedf1$group),type="s",size=2) +#group.v<-as.vector(cell_rep) +#text3d(pca$x, pca$y, pca$z, group.v, cex=1.0, adj = 1.2) # rgl.postscript("pca3d_DESeq2.pdf","pdf") ``` diff --git a/Results-template/Scripts/EdgerReport.Rmd b/Results-template/Scripts/EdgerReport.Rmd index f275e14..f82d45d 100755 --- a/Results-template/Scripts/EdgerReport.Rmd +++ b/Results-template/Scripts/EdgerReport.Rmd @@ -181,12 +181,33 @@ Phenotype=sampleinfo$condition cell_rep=sampleinfo$label tedf1$group = as.factor(Phenotype) + +pc1 = round(pca$sdev[1]^2/sum(pca$sdev^2)*100,2) +pc2 = round(pca$sdev[2]^2/sum(pca$sdev^2)*100,2) +pc3 = round(pca$sdev[3]^2/sum(pca$sdev^2)*100,2) + +pcafactor = as.factor(sampleinfo$condition) + +library(RColorBrewer) + +col <- brewer.pal(nlevels(pcafactor), "Paired") + +p <- plot_ly(as.data.frame(pca$x[,1:3]), x = ~PC1, y = ~PC2, z = ~PC3, color = pcafactor, colors = col, hoverinfo="text", + hovertext = ~sampleinfo$label) %>% + add_markers() %>% + layout(title = "PCA plot", + scene = list(xaxis = list(title = paste0("PC1 (",pc1,"%)")), + yaxis = list(title = paste0("PC2 (",pc2,"%)")), + zaxis = list(title = paste0("PC3 (",pc3,"%)")))) + +p + # plot(pca,type="lines") #Decide how many PC's are relevant for plotting #pca$x[,1:3] #look at first 3 PC's -plot3d(pca$x[,1:3],col = as.integer(tedf1$group),type="s",size=2) -group.v<-as.vector(cell_rep) -text3d(pca$x, pca$y, pca$z, group.v, cex=1.0, adj = 1.2) +#plot3d(pca$x[,1:3],col = as.integer(tedf1$group),type="s",size=2) +#group.v<-as.vector(cell_rep) +#text3d(pca$x, pca$y, pca$z, group.v, cex=1.0, adj = 1.2) # rgl.postscript("pca3d_edgeR.pdf","pdf") ``` diff --git a/Results-template/Scripts/PcaReport.Rmd b/Results-template/Scripts/PcaReport.Rmd index d6a047a..aed2d73 100755 --- a/Results-template/Scripts/PcaReport.Rmd +++ b/Results-template/Scripts/PcaReport.Rmd @@ -116,25 +116,29 @@ ddslog2= cpm(dds.ndata,log=TRUE,normalized.lib.sizes=FALSE,prior.count=0.5) ### Before Normalization ```{r, echo=FALSE, warning=FALSE,message=FALSE} -print(ggplot(melt(as.data.frame(rawlog2))) + geom_density(aes(x = value,colour = variable)) + labs(x = NULL) + theme(legend.position='right') + scale_x_log10()) +beforehist <- ggplotly(ggplot(melt(as.data.frame(rawlog2))) + geom_density(aes(x = value,colour = variable)) + labs(x = NULL) + theme(legend.position='right') + scale_x_log10()) +beforehist ``` ### TMM ```{r, echo=FALSE, warning=FALSE,message=FALSE} -print(ggplot(melt(as.data.frame(ylog2))) + geom_density(aes(x = value,colour = variable)) + labs(x = NULL) + theme(legend.position='right') + scale_x_log10()) +tmmhist <- ggplotly(ggplot(melt(as.data.frame(ylog2))) + geom_density(aes(x = value,colour = variable)) + labs(x = NULL) + theme(legend.position='right') + scale_x_log10()) +tmmhist ``` ### DESeq2 ```{r, echo=FALSE, warning=FALSE,message=FALSE} -print(ggplot(melt(as.data.frame(ddslog2))) + geom_density(aes(x = value,colour = variable)) + labs(x = NULL) + theme(legend.position='right') + scale_x_log10()) +deshist <- ggplotly(ggplot(melt(as.data.frame(ddslog2))) + geom_density(aes(x = value,colour = variable)) + labs(x = NULL) + theme(legend.position='right') + scale_x_log10()) +deshist ``` ### Limma ```{r, echo=FALSE, warning=FALSE,message=FALSE} -print(ggplot(melt(as.data.frame(v1$E))) + geom_density(aes(x = value,colour = variable)) + labs(x = NULL) + theme(legend.position='right') + scale_x_log10()) +limmahist <- ggplotly(ggplot(melt(as.data.frame(v1$E))) + geom_density(aes(x = value,colour = variable)) + labs(x = NULL) + theme(legend.position='right') + scale_x_log10()) +limmahist ``` ## **PCA Plots** {.tabset} @@ -156,16 +160,31 @@ before.pc1 = round(before.pca$sdev[1]^2/sum(before.pca$sdev^2)*100,2) before.pc2 = round(before.pca$sdev[2]^2/sum(before.pca$sdev^2)*100,2) before.pc3 = round(before.pca$sdev[3]^2/sum(before.pca$sdev^2)*100,2) +pcafactor = as.factor(sampleinfo$condition) + +library(RColorBrewer) + +col <- brewer.pal(nlevels(pcafactor), "Paired") + +p <- plot_ly(as.data.frame(before.pca$x[,1:3]), x = ~PC1, y = ~PC2, z = ~PC3, color = pcafactor, colors = col, hoverinfo="text", + hovertext = ~sampleinfo$label) %>% + add_markers() %>% + layout(title = "Before Normalization PCA plot", + scene = list(xaxis = list(title = paste0("PC1 (",before.pc1,"%)")), + yaxis = list(title = paste0("PC2 (",before.pc2,"%)")), + zaxis = list(title = paste0("PC3 (",before.pc3,"%)")))) + +p # plot(before.pca,type="lines") #Decide how many PC's are relevant for plotting #before.pca$x[,1:3] #look at first 3 PC's -plot3d(before.pca$x[,1:3],col = as.integer(before.tedf1$group),type="s",size=2,main="PCA before normalization",xlab=paste0("PC1 (",before.pc1,"%)"),ylab=paste0("PC2 (",before.pc2,"%)"),zlab=paste0("PC3 (",before.pc3,"%)")) -group.v<-as.vector(cell_rep) -text3d(before.pca$x, before.pca$y, before.pca$z, group.v, cex=1.0, adj = 1.2) -legend3d("topright", legend = levels(sampleinfo$condition), pch = 16, col = as.numeric(as.factor(levels(sampleinfo$condition))), cex=0.5) +#plot3d(before.pca$x[,1:3],col = as.integer(before.tedf1$group),type="s",size=2,main="PCA before normalization",xlab=paste0("PC1 (",before.pc1,"%)"),ylab=paste0("PC2 (",before.pc2,"%)"),zlab=paste0("PC3 (",before.pc3,"%)")) +#group.v<-as.vector(cell_rep) +#text3d(before.pca$x, before.pca$y, before.pca$z, group.v, cex=1.0, adj = 1.2) +#legend3d("topright", legend = levels(sampleinfo$condition), pch = 16, col = as.numeric(as.factor(levels(sampleinfo$condition))), cex=0.5) #rgl.postscript("pca3d_raw.pdf","pdf") -rgl.snapshot("pca3d_raw.png","png") +#rgl.snapshot("pca3d_raw.png","png") ``` @@ -186,16 +205,31 @@ edgeR.pc1 = round(edgeR.pca$sdev[1]^2/sum(edgeR.pca$sdev^2)*100,2) edgeR.pc2 = round(edgeR.pca$sdev[2]^2/sum(edgeR.pca$sdev^2)*100,2) edgeR.pc3 = round(edgeR.pca$sdev[3]^2/sum(edgeR.pca$sdev^2)*100,2) +pcafactor = as.factor(sampleinfo$condition) + +library(RColorBrewer) + +col <- brewer.pal(nlevels(pcafactor), "Paired") + +p <- plot_ly(as.data.frame(edgeR.pca$x[,1:3]), x = ~PC1, y = ~PC2, z = ~PC3, color = pcafactor, colors = col, hoverinfo="text", + hovertext = ~sampleinfo$label) %>% + add_markers() %>% + layout(title = "edgeR PCA plot", + scene = list(xaxis = list(title = paste0("PC1 (",edgeR.pc1,"%)")), + yaxis = list(title = paste0("PC2 (",edgeR.pc2,"%)")), + zaxis = list(title = paste0("PC3 (",edgeR.pc3,"%)")))) + +p # plot(edgeR.pca,type="lines") #Decide how many PC's are relevant for plotting #edgeR.pca$x[,1:3] #look at first 3 PC's -plot3d(edgeR.pca$x[,1:3],col = as.integer(edgeR.tedf1$group),type="s",size=2,main="PCA after TMM normalization",xlab=paste0("PC1 (",edgeR.pc1,"%)"),ylab=paste0("PC2 (",edgeR.pc2,"%)"),zlab=paste0("PC3 (",edgeR.pc3,"%)")) -group.v<-as.vector(cell_rep) -text3d(edgeR.pca$x, edgeR.pca$y, edgeR.pca$z, group.v, cex=1.0, adj = 1.2) -legend3d("topright", legend = levels(sampleinfo$condition), pch = 16, col = as.numeric(as.factor(levels(sampleinfo$condition))), cex=0.5) +#plot3d(edgeR.pca$x[,1:3],col = as.integer(edgeR.tedf1$group),type="s",size=2,main="PCA after TMM normalization",xlab=paste0("PC1 (",edgeR.pc1,"%)"),ylab=paste0("PC2 (",edgeR.pc2,"%)"),zlab=paste0("PC3 (",edgeR.pc3,"%)")) +#group.v<-as.vector(cell_rep) +#text3d(edgeR.pca$x, edgeR.pca$y, edgeR.pca$z, group.v, cex=1.0, adj = 1.2) +#legend3d("topright", legend = levels(sampleinfo$condition), pch = 16, col = as.numeric(as.factor(levels(sampleinfo$condition))), cex=0.5) #rgl.postscript("pca3d_edgeR.pdf","pdf") -rgl.snapshot("pca3d_edgeR.png","png") +#rgl.snapshot("pca3d_edgeR.png","png") ``` @@ -221,13 +255,28 @@ deseq2.pc1 = round(deseq2.pca$sdev[1]^2/sum(deseq2.pca$sdev^2)*100,2) deseq2.pc2 = round(deseq2.pca$sdev[2]^2/sum(deseq2.pca$sdev^2)*100,2) deseq2.pc3 = round(deseq2.pca$sdev[3]^2/sum(deseq2.pca$sdev^2)*100,2) +pcafactor = as.factor(sampleinfo$condition) + +library(RColorBrewer) -plot3d(deseq2.pca$x[,1:3],col = as.integer(deseq2.tedf1$group),type="s",size=2,main="PCA after DESeq2 normalization",xlab=paste0("PC1 (",deseq2.pc1,"%)"),ylab=paste0("PC2 (",deseq2.pc2,"%)"),zlab=paste0("PC3 (",deseq2.pc3,"%)")) -group.v<-as.vector(cell_rep) -text3d(deseq2.pca$x, deseq2.pca$y, deseq2.pca$z, group.v, cex=1.0, adj = 1.2) -legend3d("topright", legend = levels(sampleinfo$condition), pch = 16, col = as.numeric(as.factor(levels(sampleinfo$condition))), cex=0.5) +col <- brewer.pal(nlevels(pcafactor), "Paired") + +p <- plot_ly(as.data.frame(deseq2.pca$x[,1:3]), x = ~PC1, y = ~PC2, z = ~PC3, color = pcafactor, colors = col, hoverinfo="text", + hovertext = ~sampleinfo$label) %>% + add_markers() %>% + layout(title = "DESeq2 PCA plot", + scene = list(xaxis = list(title = paste0("PC1 (",deseq2.pc1,"%)")), + yaxis = list(title = paste0("PC2 (",deseq2.pc2,"%)")), + zaxis = list(title = paste0("PC3 (",deseq2.pc3,"%)")))) + +p + +#plot3d(deseq2.pca$x[,1:3],col = as.integer(deseq2.tedf1$group),type="s",size=2,main="PCA after DESeq2 normalization",xlab=paste0("PC1 (",deseq2.pc1,"%)"),ylab=paste0("PC2 (",deseq2.pc2,"%)"),zlab=paste0("PC3 (",deseq2.pc3,"%)")) +#group.v<-as.vector(cell_rep) +#text3d(deseq2.pca$x, deseq2.pca$y, deseq2.pca$z, group.v, cex=1.0, adj = 1.2) +#legend3d("topright", legend = levels(sampleinfo$condition), pch = 16, col = as.numeric(as.factor(levels(sampleinfo$condition))), cex=0.5) #rgl.postscript("pca3d_deseq2.pdf","pdf") -rgl.snapshot("pca3d_deseq2.png","png") +#rgl.snapshot("pca3d_deseq2.png","png") ``` @@ -249,13 +298,29 @@ limma.pc1 = round(limma.pca$sdev[1]^2/sum(limma.pca$sdev^2)*100,2) limma.pc2 = round(limma.pca$sdev[2]^2/sum(limma.pca$sdev^2)*100,2) limma.pc3 = round(limma.pca$sdev[3]^2/sum(limma.pca$sdev^2)*100,2) +pcafactor = as.factor(sampleinfo$condition) + +library(RColorBrewer) + +col <- brewer.pal(nlevels(pcafactor), "Paired") -plot3d(limma.pca$x[,1:3],col = as.integer(limma.tedf1$group),type="s",size=2,main="PCA after Limma normalization",xlab=paste0("PC1 (",limma.pc1,"%)"),ylab=paste0("PC2 (",limma.pc2,"%)"),zlab=paste0("PC3 (",limma.pc3,"%)")) -group.v<-as.vector(cell_rep) -text3d(limma.pca$x, limma.pca$y, limma.pca$z, group.v, cex=1.0, adj = 1.2) -legend3d("topright", legend = levels(sampleinfo$condition), pch = 16, col = as.numeric(as.factor(levels(sampleinfo$condition))), cex=0.5) +p <- plot_ly(as.data.frame(limma.pca$x[,1:3]), x = ~PC1, y = ~PC2, z = ~PC3, color = pcafactor, colors = col, hoverinfo="text", + hovertext = ~sampleinfo$label) %>% + add_markers() %>% + layout(title = "Limma PCA plot", + scene = list(xaxis = list(title = paste0("PC1 (",limma.pc1,"%)")), + yaxis = list(title = paste0("PC2 (",limma.pc2,"%)")), + zaxis = list(title = paste0("PC3 (",limma.pc3,"%)")))) + +p + + +#plot3d(limma.pca$x[,1:3],col = as.integer(limma.tedf1$group),type="s",size=2,main="PCA after Limma normalization",xlab=paste0("PC1 (",limma.pc1,"%)"),ylab=paste0("PC2 (",limma.pc2,"%)"),zlab=paste0("PC3 (",limma.pc3,"%)")) +#group.v<-as.vector(cell_rep) +#text3d(limma.pca$x, limma.pca$y, limma.pca$z, group.v, cex=1.0, adj = 1.2) +#legend3d("topright", legend = levels(sampleinfo$condition), pch = 16, col = as.numeric(as.factor(levels(sampleinfo$condition))), cex=0.5) #rgl.postscript("pca3d_limma.pdf","pdf") -rgl.snapshot("pca3d_limma.png","png") +#rgl.snapshot("pca3d_limma.png","png") ``` @@ -363,4 +428,4 @@ for(i in 1:length(sampleinfo$label)){ plotMD(v1$E,column=i, main=paste0("Limma ",sampleinfo$label[i]), xlim=c(-5,15), ylim=c(-15,15)) abline(h=0, col="red", lty=2, lwd=2) } -``` \ No newline at end of file +``` diff --git a/Results-template/Scripts/avia.pl b/Results-template/Scripts/avia.pl index aa319a8..6e76d0d 100755 --- a/Results-template/Scripts/avia.pl +++ b/Results-template/Scripts/avia.pl @@ -15,7 +15,7 @@ $cmd = ''; $time = 300; #amount of time (seconds) to wait between pings to AVIA -$cmd="/usr/local/bin/curl https://avia-abcc.ncifcrf.gov/apps/site/upload_viz -X POST -F user_file=\@$vcf -F user.ver=$species -F user_inputformat=bed -F user_api=cFMdtEdwm34iVzXOZ6 -F 'user_email=" . $email . "|nih.gov' --insecure -F user_id=$id"; +$cmd="curl https://avia-abcc.ncifcrf.gov/apps/site/upload_viz -X POST -F user_file=\@$vcf -F user.ver=$species -F user_inputformat=bed -F user_api=cFMdtEdwm34iVzXOZ6 -F 'user_email=" . $email . "|nih.gov' --insecure -F user_id=$id"; print STDERR "Executing command: $cmd\n"; @@ -39,8 +39,8 @@ while (){ chomp; last if m/^$/; - if (($_ =~ m/INFO/) || ($_ =~ m/ERROR/)) { - if ($_ =~ m/is ready for download/) { + if (($_ =~ m/INFO/) || ($_ =~ m/completed/)) { + if ($_ =~ m/completed/) { $status++; } elsif ($_ =~ m/is not accessible/) { diff --git a/Results-template/Scripts/genejunctioncounts.R b/Results-template/Scripts/genejunctioncounts.R index c523cb0..00d39f9 100755 --- a/Results-template/Scripts/genejunctioncounts.R +++ b/Results-template/Scripts/genejunctioncounts.R @@ -21,6 +21,8 @@ myfiles=as.character(unlist(strsplit(FILES, split=" "))) res=read.delim(myfiles[1],header=F,stringsAsFactors=F) stranded=res[,4] + +stranded=gsub("0",".",stranded) stranded=gsub("1","+",stranded) stranded=gsub("2","-",stranded) filler1 = rep(".",length(res[,1])) @@ -29,7 +31,7 @@ result=cbind(res[,1],res[,2],res[,3],filler1,filler2,stranded,res[,7]); tmpoutfilename1=paste(substr(myfiles[1], 0, nchar(myfiles[1])-3),"bed.recoded.tab",sep="") write.table(result,file=tmpoutfilename1,sep="\t",row.names=F,col.names=F,quote=F) tmpoutfilename2=paste(substr(myfiles[1], 0, nchar(myfiles[1])-14),"_gencodeintersects.txt",sep="") -system(paste('module load bedtools/2.19.1; bedtools intersect -a ',"gencode.gtf.filler.bed",' -b ',tmpoutfilename1,' -wao -loj -s > ',tmpoutfilename2,sep="")) +system(paste('bedtools intersect -a ',"gencode.gtf.filler.bed",' -b ',tmpoutfilename1,' -wao -loj -s > ',tmpoutfilename2,sep="")) tmpoutfilename3=paste(substr(myfiles[1], 0, nchar(myfiles[1])-14),"_genecounts.txt",sep="") system(paste('awk \'{a[$7]+=$15}END{for(i in a){print i, a[i], OFS=\"\\t\"}}\' ',tmpoutfilename2," > ",tmpoutfilename3,sep="")) tmp=read.delim(tmpoutfilename3,header=F,stringsAsFactors=F) @@ -41,6 +43,7 @@ for(i in seq(2, length(myfiles), by = 1)) { res=read.delim(myfiles[i],header=F,stringsAsFactors=F) stranded=res[,4] + stranded=gsub("0",".",stranded) stranded=gsub("1","+",stranded) stranded=gsub("2","-",stranded) filler1 = rep(".",length(res[,1])) @@ -49,7 +52,7 @@ for(i in seq(2, length(myfiles), by = 1)) tmpoutfilename1=paste(substr(myfiles[i], 0, nchar(myfiles[i])-3),"bed.recoded.tab",sep="") write.table(result,file=tmpoutfilename1,sep="\t",row.names=F,col.names=F,quote=F) tmpoutfilename2=paste(substr(myfiles[i], 0, nchar(myfiles[i])-14),"_gencodeintersects.txt",sep="") - system(paste('module load bedtools/2.19.1; bedtools intersect -a ',"gencode.gtf.filler.bed",' -b ',tmpoutfilename1,' -wao -loj -s > ',tmpoutfilename2,sep="")) + system(paste('bedtools intersect -a ',"gencode.gtf.filler.bed",' -b ',tmpoutfilename1,' -wao -loj -s > ',tmpoutfilename2,sep="")) tmpoutfilename3=paste(substr(myfiles[i], 0, nchar(myfiles[i])-14),"_genecounts.txt",sep="") system(paste('awk \'{a[$7]+=$15}END{for(i in a){print i, a[i], OFS=\"\\t\"}}\' ',tmpoutfilename2," > ",tmpoutfilename3,sep="")) tmp=read.delim(tmpoutfilename3,header=F,stringsAsFactors=F) diff --git a/Results-template/Scripts/karyoplot.py b/Results-template/Scripts/karyoplot.py index 3559d7b..07772e9 100755 --- a/Results-template/Scripts/karyoplot.py +++ b/Results-template/Scripts/karyoplot.py @@ -8,6 +8,28 @@ import numpy plt.switch_backend('agg') +def findChromosomes(karyofn): + fh = open(karyofn) + p1List, p2List,p3List = [], [], [] + + for line in fh: + linelist = line.strip().split() + chromosome = linelist[0].lstrip("chr") + try: + int(chromosome) + if chromosome not in p1List and int(chromosome) <= 12: + p1List.append(chromosome) + elif chromosome not in p2List and int(chromosome) >=13: + p2List.append(chromosome) + except ValueError: + if chromosome not in p3List and (chromosome == "Y" or chromosome == "X"): + p3List.append(chromosome) + + fh.close() + + print(p1List,p2List,p3List) + return p1List, p2List, p3List + def karyoplot(karyo_filename, metadata={}, part=1): ''' To create a karyo_filename go to: http://genome.ucsc.edu/cgi-bin/hgTables @@ -45,8 +67,14 @@ def karyoplot(karyo_filename, metadata={}, part=1): ax.set_ylim([0.0, DIM]) def get_chromosome_length(chromosome): - chromosome_start = float(min([x[1] for x in karyo_dict[chromosome]])) - chromosome_end = float(max(x[2] for x in karyo_dict[chromosome])) + + try: + chromosome_start = float(min([x[1] for x in karyo_dict[chromosome]])) + chromosome_end = float(max(x[2] for x in karyo_dict[chromosome])) + + except ValueError: + chromosome_start = 0.0 # no differentially expressed regions, dummy value + chromosome_end = 1000000.0 # no differentially expressed regions, dummy value chromosome_length = chromosome_end - chromosome_start #return int(chromosome_length*1.05) @@ -145,37 +173,51 @@ def plot_chromosome(chromosome, order): ax.text(x_start, y_end - (DIM * 0.07), chromosome) + + p1,p2,p3 = findChromosomes(karyo_filename) if part==1: - plot_chromosome('1', 1) - plot_chromosome('2', 2) - plot_chromosome('3', 3) - plot_chromosome('4', 4) - plot_chromosome('5', 5) - plot_chromosome('6', 6) - plot_chromosome('7', 7) - plot_chromosome('8', 8) - plot_chromosome('9', 9) - plot_chromosome('10', 10) - plot_chromosome('11', 11) - plot_chromosome('12', 12) + for chromNUM in sorted(p1): + plot_chromosome(str(chromNUM), int(chromNUM)) + #plot_chromosome('1', 1) + #plot_chromosome('2', 2) + #plot_chromosome('3', 3) + #plot_chromosome('4', 4) + #plot_chromosome('5', 5) + #plot_chromosome('6', 6) + #plot_chromosome('7', 7) + #plot_chromosome('8', 8) + #plot_chromosome('9', 9) + #plot_chromosome('10', 10) + #plot_chromosome('11', 11) + #plot_chromosome('12', 12) elif part==2: - plot_chromosome('13', 1) - plot_chromosome('14', 2) - plot_chromosome('15', 3) - plot_chromosome('16', 4) - plot_chromosome('17', 5) - plot_chromosome('18', 6) - plot_chromosome('19', 7) + counter = 1 + for chromNUM in sorted(p2): + plot_chromosome(str(chromNUM), counter) + counter += 1 + + if "X" or "x" in p3: + plot_chromosome('X', 11) + elif "Y" or "y" in p3: + plot_chromosome('Y', 12) + + #plot_chromosome('13', 1) + #plot_chromosome('14', 2) + #plot_chromosome('15', 3) + #plot_chromosome('16', 4) + #plot_chromosome('17', 5) + #plot_chromosome('18', 6) + #plot_chromosome('19', 7) - if "hg" in species: - plot_chromosome('20', 8) - plot_chromosome('21', 9) - plot_chromosome('22', 10) + #if "hg" in species: + #plot_chromosome('20', 8) + #plot_chromosome('21', 9) + #plot_chromosome('22', 10) - plot_chromosome('X', 11) - plot_chromosome('Y', 12) + #plot_chromosome('X', 11) + #plot_chromosome('Y', 12) elif part==0: #print("HERE1") @@ -189,7 +231,9 @@ def plot_chromosome(chromosome, order): return import sys +print(sys.argv) fn = sys.argv[1] +findChromosomes(fn) species = sys.argv[2] #print('plotting..') karyoplot(fn, part=1) diff --git a/Results-template/Scripts/maftools.R b/Results-template/Scripts/maftools.R index a25e0e7..876b0af 100644 --- a/Results-template/Scripts/maftools.R +++ b/Results-template/Scripts/maftools.R @@ -6,7 +6,9 @@ FILE2 <- args[3] FILE3 <- args[4] setwd(DIR) mymaf <- read.maf(FILE1) -plotmafSummary(mymaf,file=FILE2) +pdf(FILE2) +plotmafSummary(mymaf) +dev.off() pdf(FILE3) oncoplot(mymaf,writeMatrix=TRUE,showTumorSampleBarcodes=TRUE) dev.off() \ No newline at end of file diff --git a/Results-template/Scripts/make_sample_network.pl b/Results-template/Scripts/make_sample_network.pl index 5bd8d74..59665b0 100755 --- a/Results-template/Scripts/make_sample_network.pl +++ b/Results-template/Scripts/make_sample_network.pl @@ -12,9 +12,9 @@ $cmd = 'module load vcftools; vcftools --vcf ' . $vcf . ' --plink --remove-indels --out plink'; system($cmd); -$cmd = 'module load plink/1.07; plink --file plink --distance-matrix --out distance --cluster'; +$cmd = 'module load plink/1.9.0-beta4.4; plink --file plink --distance-matrix --out distance'; system($cmd); -$cmd = 'cut -f 1 -d \' \' distance.cluster2 > samples.txt'; +$cmd = 'cut -f 1 -d \' \' distance.mdist.id > samples.txt'; system($cmd); #open directory (SWITCH CHROMOSOME ARM HERE) @@ -73,9 +73,9 @@ } close O; -$cmd = 'module load phylip; neighbor << EOF' . "\n" . 'distance.matrix' . "\n" . "N\nY\nEOF"; +$cmd = 'module load phylip/3.697; neighbor << EOF' . "\n" . 'distance.matrix' . "\n" . "N\nY\nEOF"; system($cmd); -$cmd = 'module load phylip; drawtree << EOF' . "\nouttree\n" . 'Scripts/fontfile' . "\nP\nW\n3000\n3000\nC\n" . '0.75' . "\nL\nR\nY\nEOF"; +$cmd = 'module load phylip/3.697; drawtree << EOF' . "\nouttree\n" . 'Scripts/fontfile' . "\nP\nW\n3000\n3000\nC\n" . '0.75' . "\nL\nR\nY\nEOF"; system($cmd); $cmd = 'mv plotfile sample_network.bmp'; system($cmd); \ No newline at end of file diff --git a/Rules/CAPmirseq-plus.snakefile b/Rules/CAPmirseq-plus.snakefile index d175e8e..4b04dc0 100755 --- a/Rules/CAPmirseq-plus.snakefile +++ b/Rules/CAPmirseq-plus.snakefile @@ -179,7 +179,7 @@ rule mirseq_mirdeep2: shell: """ ###module load viennarna -module load bowtie/1.1.1 +module load bowtie/1.2.2 module load randfold module load mirdeep diff --git a/Rules/InitialChIPseqQC.snakefile b/Rules/InitialChIPseqQC.snakefile index ce75950..62f363c 100644 --- a/Rules/InitialChIPseqQC.snakefile +++ b/Rules/InitialChIPseqQC.snakefile @@ -160,7 +160,6 @@ fastqc {input} -t {threads} -o {output} picardver=config['bin'][pfamily]['tool_versions']['PICARDVER'], bwaver=config['bin'][pfamily]['tool_versions']['BWAVER'], parallelver=config['bin'][pfamily]['tool_versions']['PARALLELVER'], - pigzver=config['bin'][pfamily]['tool_versions']['PIGZVER'], samtoolsver=config['bin'][pfamily]['tool_versions']['SAMTOOLSVER'], minlen=config['bin'][pfamily]['tool_parameters']['MINLEN'], javaram="64g", @@ -168,7 +167,6 @@ fastqc {input} -t {threads} -o {output} shell: """ module load {params.cutadaptver}; module load {params.parallelver}; -module load {params.pigzver}; if [ ! -e /lscratch/$SLURM_JOBID ]; then mkdir /lscratch/$SLURM_JOBID ;fi cd /lscratch/$SLURM_JOBID sample=`echo {input.infq}|awk -F "/" '{{print $NF}}'|awk -F ".R1.fastq" '{{print $1}}'` @@ -333,7 +331,7 @@ samtools flagstat {output.outbam2} > {output.flagstat2} picardver=config['bin'][pfamily]['PICARDVER'], shell: """ - module load samtools/1.5; + module load samtools/1.6; samtools flagstat {input.file1} > {output.outstar2}; echo 0 >> {output.outstar2}; echo 0 >> {output.outstar2}; @@ -419,7 +417,6 @@ fastqc {input} -t {threads} -o {output}; blacklistbwaindex=config['references'][pfamily]['BLACKLISTBWAINDEX'], picardver=config['bin'][pfamily]['tool_versions']['PICARDVER'], parallelver=config['bin'][pfamily]['tool_versions']['PARALLELVER'], - pigzver=config['bin'][pfamily]['tool_versions']['PIGZVER'], bwaver=config['bin'][pfamily]['tool_versions']['BWAVER'], samtoolsver=config['bin'][pfamily]['tool_versions']['SAMTOOLSVER'], minlen=config['bin'][pfamily]['tool_parameters']['MINLEN'], @@ -428,7 +425,6 @@ fastqc {input} -t {threads} -o {output}; shell: """ module load {params.cutadaptver}; module load {params.parallelver}; -module load {params.pigzver}; if [ ! -e /lscratch/$SLURM_JOBID ]; then mkdir /lscratch/$SLURM_JOBID ;fi cd /lscratch/$SLURM_JOBID sample=`echo {input.file1}|awk -F "/" '{{print $NF}}'|awk -F ".R1.fastq" '{{print $1}}'` diff --git a/Rules/admixture_germline.rl b/Rules/admixture_germline.rl index be53061..4dadf50 100755 --- a/Rules/admixture_germline.rl +++ b/Rules/admixture_germline.rl @@ -10,6 +10,6 @@ rule admixture_germline: params: gatk=config['bin'][pfamily]['GATK'],ref=config['project']['annotation'],genome=config['references'][pfamily]['GENOME'],key=config['references'][pfamily]['ADMIXTUREKEY'],refcount=config['references'][pfamily]['ADMIXTUREREFS'],knowns=config['references'][pfamily]['KNOWNANCESTRY'],rname="admixture" threads: 8 shell: """ - mkdir -p admixture_out; module load vcftools; vcftools --vcf {input} --remove-indels --max-missing 1 --recode --recode-INFO-all --out admixture_out/samples_noINDEL_nomissing; module load GATK/3.5-0; GATK -m 48G CombineVariants -R {params.genome} --genotypemergeoption UNSORTED -o {output.mergedvcf} --variant {params.knowns} --variant {input} --minimumN 2 -nt 4; vcftools --vcf {output.mergedvcf} --maf 0.05 --remove-indels --plink --out admixture_out/samples_and_knowns_filtered; module load plink/1.07; plink --noweb --recode12 --out admixture_out/samples_and_knowns_filtered_recode --file admixture_out/samples_and_knowns_filtered; perl Scripts/admixture_prep.pl {params.key} admixture_out/samples_and_knowns_filtered_recode.pop admixture_out/samples_and_knowns_filtered_recode.ped; /data/CCBR_Pipeliner/db/PipeDB/bin/admixture_linux-1.3.0/admixture admixture_out/samples_and_knowns_filtered_recode.ped {params.refcount} --supervised -j32; mv samples_and_knowns_filtered_recode.{params.refcount}.P admixture_out/samples_and_knowns_filtered_recode.P; mv samples_and_knowns_filtered_recode.{params.refcount}.Q admixture_out/samples_and_knowns_filtered_recode.Q; perl Scripts/admixture_post.pl {params.key} {output.table} {output.admix} {params.ref} {output.recodeped} + mkdir -p admixture_out; module load vcftools; vcftools --vcf {input} --remove-indels --max-missing 1 --recode --recode-INFO-all --out admixture_out/samples_noINDEL_nomissing; module load GATK/3.5-0; GATK -m 48G CombineVariants -R {params.genome} --genotypemergeoption UNSORTED -o {output.mergedvcf} --variant {params.knowns} --variant {input} --minimumN 2 -nt 4; vcftools --vcf {output.mergedvcf} --maf 0.05 --remove-indels --plink --out admixture_out/samples_and_knowns_filtered; module load plink/1.9.0-beta4.4; plink --noweb --recode12 --out admixture_out/samples_and_knowns_filtered_recode --file admixture_out/samples_and_knowns_filtered; perl Scripts/admixture_prep.pl {params.key} admixture_out/samples_and_knowns_filtered_recode.pop admixture_out/samples_and_knowns_filtered_recode.ped; /data/CCBR_Pipeliner/db/PipeDB/bin/admixture_linux-1.3.0/admixture admixture_out/samples_and_knowns_filtered_recode.ped {params.refcount} --supervised -j32; mv samples_and_knowns_filtered_recode.{params.refcount}.P admixture_out/samples_and_knowns_filtered_recode.P; mv samples_and_knowns_filtered_recode.{params.refcount}.Q admixture_out/samples_and_knowns_filtered_recode.Q; perl Scripts/admixture_post.pl {params.key} {output.table} {output.admix} {params.ref} {output.recodeped} """ \ No newline at end of file diff --git a/Rules/admixture_somatic.rl b/Rules/admixture_somatic.rl index d05f902..b3160f0 100644 --- a/Rules/admixture_somatic.rl +++ b/Rules/admixture_somatic.rl @@ -10,6 +10,6 @@ rule admixture_somatic: params: gatk=config['bin'][pfamily]['GATK'],ref=config['project']['annotation'],regions="exome_targets.bed",genome=config['references'][pfamily]['GENOME'],key=config['references'][pfamily]['ADMIXTUREKEY'],refcount=config['references'][pfamily]['ADMIXTUREREFS'],knowns=config['references'][pfamily]['KNOWNANCESTRY'],rname="admixture" threads: 8 shell: """ - mkdir -p admixture_out; module load vcftools; vcftools --vcf {input} --remove-indels --max-missing 1 --recode --recode-INFO-all --out admixture_out/samples_noINDEL_nomissing; module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T CombineVariants -R {params.genome} --genotypemergeoption UNSORTED -o {output.mergedvcf} --variant {params.knowns} --variant {input} -L {params.regions} --minimumN 2 -nt 1; vcftools --vcf {output.mergedvcf} --maf 0.05 --remove-indels --plink --out admixture_out/samples_and_knowns_filtered; module load plink/1.07; plink --noweb --recode12 --out admixture_out/samples_and_knowns_filtered_recode --file admixture_out/samples_and_knowns_filtered; perl Scripts/admixture_prep.pl {params.key} admixture_out/samples_and_knowns_filtered_recode.pop admixture_out/samples_and_knowns_filtered_recode.ped; /data/CCBR_Pipeliner/db/PipeDB/bin/admixture_linux-1.3.0/admixture admixture_out/samples_and_knowns_filtered_recode.ped {params.refcount} --supervised -j32; mv samples_and_knowns_filtered_recode.{params.refcount}.P admixture_out/samples_and_knowns_filtered_recode.P; mv samples_and_knowns_filtered_recode.{params.refcount}.Q admixture_out/samples_and_knowns_filtered_recode.Q; perl Scripts/admixture_post.pl {params.key} {output.table} {output.admix} {params.ref} {output.recodeped} + mkdir -p admixture_out; module load vcftools; vcftools --vcf {input} --remove-indels --max-missing 1 --recode --recode-INFO-all --out admixture_out/samples_noINDEL_nomissing; module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T CombineVariants -R {params.genome} --genotypemergeoption UNSORTED -o {output.mergedvcf} --variant {params.knowns} --variant {input} -L {params.regions} --minimumN 2 -nt 1; vcftools --vcf {output.mergedvcf} --maf 0.05 --remove-indels --plink --out admixture_out/samples_and_knowns_filtered; module load plink/1.9.0-beta4.4; plink --noweb --recode12 --out admixture_out/samples_and_knowns_filtered_recode --file admixture_out/samples_and_knowns_filtered; perl Scripts/admixture_prep.pl {params.key} admixture_out/samples_and_knowns_filtered_recode.pop admixture_out/samples_and_knowns_filtered_recode.ped; /data/CCBR_Pipeliner/db/PipeDB/bin/admixture_linux-1.3.0/admixture admixture_out/samples_and_knowns_filtered_recode.ped {params.refcount} --supervised -j32; mv samples_and_knowns_filtered_recode.{params.refcount}.P admixture_out/samples_and_knowns_filtered_recode.P; mv samples_and_knowns_filtered_recode.{params.refcount}.Q admixture_out/samples_and_knowns_filtered_recode.Q; perl Scripts/admixture_post.pl {params.key} {output.table} {output.admix} {params.ref} {output.recodeped} """ \ No newline at end of file diff --git a/Rules/admixture_wgs.rl b/Rules/admixture_wgs.rl index ef9a324..c24f57b 100644 --- a/Rules/admixture_wgs.rl +++ b/Rules/admixture_wgs.rl @@ -10,6 +10,6 @@ rule admixture_wgs: params: gatk=config['bin'][pfamily]['GATK'],ref=config['project']['annotation'],genome=config['references'][pfamily]['GENOME'],key=config['references'][pfamily]['ADMIXTUREKEY'],refcount=config['references'][pfamily]['ADMIXTUREREFS'],knowns=config['references'][pfamily]['KNOWNANCESTRY'],rname="admixture" threads: 8 shell: """ - mkdir -p admixture_out; module load vcftools; vcftools --vcf {input} --remove-indels --max-missing 1 --recode --recode-INFO-all --out admixture_out/samples_noINDEL_nomissing; module load GATK/3.5-0; GATK -m 48G CombineVariants -R {params.genome} --genotypemergeoption UNSORTED -o {output.mergedvcf} --variant {params.knowns} --variant {input} --minimumN 2 -nt 4; vcftools --vcf {output.mergedvcf} --maf 0.05 --remove-indels --plink --out admixture_out/samples_and_knowns_filtered; module load plink/1.07; plink --noweb --recode12 --out admixture_out/samples_and_knowns_filtered_recode --file admixture_out/samples_and_knowns_filtered; perl Scripts/admixture_prep.pl {params.key} admixture_out/samples_and_knowns_filtered_recode.pop admixture_out/samples_and_knowns_filtered_recode.ped; /data/CCBR_Pipeliner/db/PipeDB/bin/admixture_linux-1.3.0/admixture admixture_out/samples_and_knowns_filtered_recode.ped {params.refcount} --supervised -j32; mv samples_and_knowns_filtered_recode.{params.refcount}.P admixture_out/samples_and_knowns_filtered_recode.P; mv samples_and_knowns_filtered_recode.{params.refcount}.Q admixture_out/samples_and_knowns_filtered_recode.Q; perl Scripts/admixture_post.pl {params.key} {output.table} {output.admix} {params.ref} {output.recodeped} + mkdir -p admixture_out; module load vcftools; vcftools --vcf {input} --remove-indels --max-missing 1 --recode --recode-INFO-all --out admixture_out/samples_noINDEL_nomissing; module load GATK/3.5-0; GATK -m 48G CombineVariants -R {params.genome} --genotypemergeoption UNSORTED -o {output.mergedvcf} --variant {params.knowns} --variant {input} --minimumN 2 -nt 4; vcftools --vcf {output.mergedvcf} --maf 0.05 --remove-indels --plink --out admixture_out/samples_and_knowns_filtered; module load plink/1.9.0-beta4.4; plink --noweb --recode12 --out admixture_out/samples_and_knowns_filtered_recode --file admixture_out/samples_and_knowns_filtered; perl Scripts/admixture_prep.pl {params.key} admixture_out/samples_and_knowns_filtered_recode.pop admixture_out/samples_and_knowns_filtered_recode.ped; /data/CCBR_Pipeliner/db/PipeDB/bin/admixture_linux-1.3.0/admixture admixture_out/samples_and_knowns_filtered_recode.ped {params.refcount} --supervised -j32; mv samples_and_knowns_filtered_recode.{params.refcount}.P admixture_out/samples_and_knowns_filtered_recode.P; mv samples_and_knowns_filtered_recode.{params.refcount}.Q admixture_out/samples_and_knowns_filtered_recode.Q; perl Scripts/admixture_post.pl {params.key} {output.table} {output.admix} {params.ref} {output.recodeped} """ \ No newline at end of file diff --git a/Rules/admixture_wgs_somatic.rl b/Rules/admixture_wgs_somatic.rl index 8b546c3..b9aff9a 100644 --- a/Rules/admixture_wgs_somatic.rl +++ b/Rules/admixture_wgs_somatic.rl @@ -10,6 +10,6 @@ rule admixture_wgs_somatic: params: gatk=config['bin'][pfamily]['GATK'],ref=config['project']['annotation'],genome=config['references'][pfamily]['GENOME'],key=config['references'][pfamily]['ADMIXTUREKEY'],refcount=config['references'][pfamily]['ADMIXTUREREFS'],knowns=config['references'][pfamily]['KNOWNANCESTRY'],rname="admixture" threads: 8 shell: """ - mkdir -p admixture_out; module load vcftools; vcftools --vcf {input} --remove-indels --max-missing 1 --recode --recode-INFO-all --out admixture_out/samples_noINDEL_nomissing; module load GATK/3.5-0; GATK -m 48G CombineVariants -R {params.genome} --genotypemergeoption UNSORTED -o {output.mergedvcf} --variant {params.knowns} --variant {input} --minimumN 2 -nt 4; vcftools --vcf {output.mergedvcf} --maf 0.05 --remove-indels --plink --out admixture_out/samples_and_knowns_filtered; module load plink/1.07; plink --noweb --recode12 --out admixture_out/samples_and_knowns_filtered_recode --file admixture_out/samples_and_knowns_filtered; perl Scripts/admixture_prep.pl {params.key} admixture_out/samples_and_knowns_filtered_recode.pop admixture_out/samples_and_knowns_filtered_recode.ped; /data/CCBR_Pipeliner/db/PipeDB/bin/admixture_linux-1.3.0/admixture admixture_out/samples_and_knowns_filtered_recode.ped {params.refcount} --supervised -j32; mv samples_and_knowns_filtered_recode.{params.refcount}.P admixture_out/samples_and_knowns_filtered_recode.P; mv samples_and_knowns_filtered_recode.{params.refcount}.Q admixture_out/samples_and_knowns_filtered_recode.Q; perl Scripts/admixture_post.pl {params.key} {output.table} {output.admix} {params.ref} {output.recodeped} + mkdir -p admixture_out; module load vcftools; vcftools --vcf {input} --remove-indels --max-missing 1 --recode --recode-INFO-all --out admixture_out/samples_noINDEL_nomissing; module load GATK/3.5-0; GATK -m 48G CombineVariants -R {params.genome} --genotypemergeoption UNSORTED -o {output.mergedvcf} --variant {params.knowns} --variant {input} --minimumN 2 -nt 4; vcftools --vcf {output.mergedvcf} --maf 0.05 --remove-indels --plink --out admixture_out/samples_and_knowns_filtered; module load plink/1.9.0-beta4.4; plink --noweb --recode12 --out admixture_out/samples_and_knowns_filtered_recode --file admixture_out/samples_and_knowns_filtered; perl Scripts/admixture_prep.pl {params.key} admixture_out/samples_and_knowns_filtered_recode.pop admixture_out/samples_and_knowns_filtered_recode.ped; /data/CCBR_Pipeliner/db/PipeDB/bin/admixture_linux-1.3.0/admixture admixture_out/samples_and_knowns_filtered_recode.ped {params.refcount} --supervised -j32; mv samples_and_knowns_filtered_recode.{params.refcount}.P admixture_out/samples_and_knowns_filtered_recode.P; mv samples_and_knowns_filtered_recode.{params.refcount}.Q admixture_out/samples_and_knowns_filtered_recode.Q; perl Scripts/admixture_post.pl {params.key} {output.table} {output.admix} {params.ref} {output.recodeped} """ \ No newline at end of file diff --git a/Rules/all-exomeseq-germline.rl b/Rules/all-exomeseq-germline.rl index 9c865db..97fe4cc 100755 --- a/Rules/all-exomeseq-germline.rl +++ b/Rules/all-exomeseq-germline.rl @@ -13,6 +13,6 @@ rule all_exomeseq_germline: output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ """ \ No newline at end of file diff --git a/Rules/all-exomeseq-somatic-tumoronly.rl b/Rules/all-exomeseq-somatic-tumoronly.rl index 039423d..44feb67 100644 --- a/Rules/all-exomeseq-somatic-tumoronly.rl +++ b/Rules/all-exomeseq-somatic-tumoronly.rl @@ -22,7 +22,7 @@ if config['project']['annotation'] == "hg19": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ @@ -50,7 +50,7 @@ elif config['project']['annotation'] == "hg38": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ @@ -77,6 +77,6 @@ elif config['project']['annotation'] == "mm10": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ \ No newline at end of file diff --git a/Rules/all-exomeseq-somatic.rl b/Rules/all-exomeseq-somatic.rl index 6806d8e..83d9f25 100755 --- a/Rules/all-exomeseq-somatic.rl +++ b/Rules/all-exomeseq-somatic.rl @@ -44,7 +44,7 @@ if config['project']['annotation'] == "hg19": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ elif config['project']['annotation'] == "hg38": @@ -93,7 +93,7 @@ elif config['project']['annotation'] == "hg38": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ @@ -139,6 +139,6 @@ elif config['project']['annotation'] == "mm10": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ \ No newline at end of file diff --git a/Rules/all-initialqc.rl b/Rules/all-initialqc.rl index e9bd028..4c133b0 100755 --- a/Rules/all-initialqc.rl +++ b/Rules/all-initialqc.rl @@ -12,11 +12,11 @@ rule all_initialqc: "multiqc_report.html", expand("QC/{s}_run_trimmomatic.err",s=samples), expand("QC/{s}.qualimapReport/genome_results.txt",s=samples), - config['project']['id']+"_"+config['project']['flowcellid']+".xlsx", +# config['project']['id']+"_"+config['project']['flowcellid']+".xlsx", config['project']['workpath']+"/exome_targets.bed" output: params: rname="final" shell: """ - mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *bam_stats bamstats/; mv *.bam_stats.err bamstats/; mv *.bam.err bamstats/; rm *sorted.bam.bai; mv *sorted.txt logfiles/ + mv *.out slurmfiles/; perl Scripts/summarize_usage.pl """ \ No newline at end of file diff --git a/Rules/all-rnafusion.rl b/Rules/all-rnafusion.rl index af527ba..0de497f 100644 --- a/Rules/all-rnafusion.rl +++ b/Rules/all-rnafusion.rl @@ -35,7 +35,7 @@ if config['project']['annotation'] == "hg19": output: params: rname="final" shell: """ - Scripts/fusionSummary.sh; module load multiqc/1.1; multiqc -f .; rm *featureCounts; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl + Scripts/fusionSummary.sh; module load multiqc/1.4; multiqc -f .; rm *featureCounts; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl """ @@ -76,7 +76,7 @@ elif config['project']['annotation'] == "hg38": output: params: rname="final" shell: """ - Scripts/fusionSummary.sh; module load multiqc/1.1; multiqc -f .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl + Scripts/fusionSummary.sh; module load multiqc/1.4; multiqc -f .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl """ @@ -113,6 +113,6 @@ elif config['project']['annotation'] == "mm10": output: params: rname="final" shell: """ - Scripts/fusionSummary.sh; module load multiqc/1.1; multiqc -f .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl + Scripts/fusionSummary.sh; module load multiqc/1.4; multiqc -f .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl """ \ No newline at end of file diff --git a/Rules/all-rnaseqvar-somatic.rl b/Rules/all-rnaseqvar-somatic.rl index c2a9b03..8b789f3 100755 --- a/Rules/all-rnaseqvar-somatic.rl +++ b/Rules/all-rnaseqvar-somatic.rl @@ -41,6 +41,6 @@ rule all_exomeseq_somatic: output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ """ \ No newline at end of file diff --git a/Rules/all-rnaseqvargerm.rl b/Rules/all-rnaseqvargerm.rl index 081ea5a..bc0132f 100755 --- a/Rules/all-rnaseqvargerm.rl +++ b/Rules/all-rnaseqvargerm.rl @@ -14,6 +14,6 @@ rule all_rnaseqvargerm: output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; rm *sorted.bam.bai; mv *sorted.txt logfiles/; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; mv *.fin.bam.intervals logfiles/; rm *realign.bai; rm *sorted.bam.bai; mv *sorted.txt logfiles/; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ """ \ No newline at end of file diff --git a/Rules/all-wgs-somatic-tumoronly.rl b/Rules/all-wgs-somatic-tumoronly.rl index 0e078a5..95fd1ea 100644 --- a/Rules/all-wgs-somatic-tumoronly.rl +++ b/Rules/all-wgs-somatic-tumoronly.rl @@ -21,7 +21,7 @@ if config['project']['annotation'] == "hg19": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ elif config['project']['annotation'] == "hg38": @@ -47,7 +47,7 @@ elif config['project']['annotation'] == "hg38": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ @@ -72,6 +72,6 @@ elif config['project']['annotation'] == "mm10": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ \ No newline at end of file diff --git a/Rules/all-wgs-somatic.rl b/Rules/all-wgs-somatic.rl index 2c2dfda..e4ee91e 100644 --- a/Rules/all-wgs-somatic.rl +++ b/Rules/all-wgs-somatic.rl @@ -45,7 +45,7 @@ if config['project']['annotation'] == "hg19": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ elif config['project']['annotation'] == "hg38": @@ -95,7 +95,7 @@ elif config['project']['annotation'] == "hg38": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ @@ -142,6 +142,6 @@ elif config['project']['annotation'] == "mm10": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped logfiles/ """ \ No newline at end of file diff --git a/Rules/all-wgslow.rl b/Rules/all-wgslow.rl index 71afdd4..7cec3b6 100755 --- a/Rules/all-wgslow.rl +++ b/Rules/all-wgslow.rl @@ -47,7 +47,7 @@ if config['project']['annotation'] == "hg19": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ """ @@ -100,7 +100,7 @@ elif config['project']['annotation'] == "hg38": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ """ @@ -148,6 +148,6 @@ elif config['project']['annotation'] == "mm10": output: params: rname="final" shell: """ - module load multiqc/1.1; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ + module load multiqc/1.4; multiqc -f -e featureCounts .; mv *.out slurmfiles/; perl Scripts/summarize_usage.pl; rm *realign.bai; mv distance.cluster0 distance.cluster1 distance.cluster2 distance.cluster3 distance.nosex samples.txt plink.map plink.ped *.avia_status.txt *.avia.log *_genotypes.vcf logfiles/ """ \ No newline at end of file diff --git a/Rules/avia.rl b/Rules/avia.rl index 39477f1..f2dccb0 100755 --- a/Rules/avia.rl +++ b/Rules/avia.rl @@ -3,7 +3,7 @@ rule avia: output:config['project']['workpath']+"/full_annot.txt.zip" params: batch ="-l nodes=1:gpfs -q ccr",email=config['project']['username'],species=config['references'][pfamily]['AVIASET'],rname="avia" shell: """ - module load perl/5.18.2; perl Scripts/avia.pl {input} {params.email} {params.species} + module load perl/5.18.4; perl Scripts/avia.pl {input} {params.email} {params.species} """ diff --git a/Rules/bwa.mem.rl b/Rules/bwa.mem.rl index 969c907..73e100d 100755 --- a/Rules/bwa.mem.rl +++ b/Rules/bwa.mem.rl @@ -4,6 +4,6 @@ rule bwa_mem: params: bwa=config['bin'][pfamily]['BWA'],ref=config['references'][pfamily]['BWAGENOME'],sam=config['bin'][pfamily]['SAMTOOLS'],rname="pl:bwamem" threads: 32 shell: """ - module load samtools; {params.bwa} mem -M -t {threads} {params.ref} {input} | samtools view -bS - > {output} + module load samtools/1.8; module load bwa/0.7.17; bwa mem -M -t {threads} {params.ref} {input} | samtools view -bS - > {output} """ diff --git a/Rules/canvas_wgs_germ.rl b/Rules/canvas_wgs_germ.rl index 933e07a..92ea907 100644 --- a/Rules/canvas_wgs_germ.rl +++ b/Rules/canvas_wgs_germ.rl @@ -3,4 +3,4 @@ rule canvas_wgs_germ: vcf="sample_vcfs/{x}.sample.vcf", output: vcf="canvas_out/{x}/CNV.vcf.gz", params: genome=config['references'][pfamily]['CANVASGENOME'],sample=lambda wildcards: config['project']['units'][wildcards.x],kmer=config['references'][pfamily]['CANVASKMER'],filter=config['references'][pfamily]['CANVASFILTER'],rname="pl:canvas" - shell: "mkdir -p canvas_out; mkdir -p canvas_out/{params.sample}; cp {params.sample}.recal.bai {params.sample}.recal.bam.bai; export COMPlus_gcAllowVeryLargeObjects=1; module load Canvas/1.25; Canvas.dll Germline-WGS -b {input.bam} -o canvas_out/{params.sample} -r {params.kmer} -g {params.genome} -f {params.filter} --sample-name={params.sample} --sample-b-allele-vcf={input.vcf}" \ No newline at end of file + shell: "mkdir -p canvas_out; mkdir -p canvas_out/{params.sample}; cp {params.sample}.recal.bai {params.sample}.recal.bam.bai; export COMPlus_gcAllowVeryLargeObjects=1; module load Canvas/1.31; Canvas.dll Germline-WGS -b {input.bam} -o canvas_out/{params.sample} -r {params.kmer} -g {params.genome} -f {params.filter} --sample-name={params.sample} --sample-b-allele-vcf={input.vcf}" \ No newline at end of file diff --git a/Rules/canvas_wgs_somatic.rl b/Rules/canvas_wgs_somatic.rl index 787d313..7aaa542 100644 --- a/Rules/canvas_wgs_somatic.rl +++ b/Rules/canvas_wgs_somatic.rl @@ -6,4 +6,4 @@ rule canvas_wgs_somatic: output: tumorvcf="canvas_out/{x}/tumor_CNV.vcf.gz", normvcf="canvas_out/{x}/normal_CNV.vcf.gz", params: genome=config['references'][pfamily]['CANVASGENOME'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],kmer=config['references'][pfamily]['CANVASKMER'],filter=config['references'][pfamily]['CANVASFILTER'],balleles=config['references'][pfamily]['KNOWNVCF2'],rname="pl:canvas" - shell: "mkdir -p canvas_out; mkdir -p canvas_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample}; cp {params.tumorsample}.recal.bai {params.tumorsample}.recal.bam.bai; cp {params.normalsample}.recal.bai {params.normalsample}.recal.bam.bai; mkdir -p canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}; export COMPlus_gcAllowVeryLargeObjects=1; module load Canvas/1.25; Canvas.dll Somatic-WGS -b {input.tumor} -o canvas_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample} -r {params.kmer} -g {params.genome} -f {params.filter} --sample-name={params.tumorsample} --population-b-allele-vcf={params.balleles} --somatic-vcf={input.somaticvcf}; module load vcftools; vcftools --vcf {input.bvcf} --indv {params.normalsample} --recode --recode-INFO-all --out canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}/{params.normalsample}; Canvas.dll Germline-WGS -b {input.normal} -o canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample} -r {params.kmer} -g {params.genome} -f {params.filter} --sample-name={params.normalsample} --sample-b-allele-vcf=canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}/{params.normalsample}.recode.vcf; mv canvas_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample}/CNV.vcf.gz canvas_out/{params.normalsample}+{params.tumorsample}/tumor_CNV.vcf.gz; mv canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}/CNV.vcf.gz canvas_out/{params.normalsample}+{params.tumorsample}/normal_CNV.vcf.gz" \ No newline at end of file + shell: "mkdir -p canvas_out; mkdir -p canvas_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample}; cp {params.tumorsample}.recal.bai {params.tumorsample}.recal.bam.bai; cp {params.normalsample}.recal.bai {params.normalsample}.recal.bam.bai; mkdir -p canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}; export COMPlus_gcAllowVeryLargeObjects=1; module load Canvas/1.31; Canvas.dll Somatic-WGS -b {input.tumor} -o canvas_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample} -r {params.kmer} -g {params.genome} -f {params.filter} --sample-name={params.tumorsample} --population-b-allele-vcf={params.balleles} --somatic-vcf={input.somaticvcf}; module load vcftools; vcftools --vcf {input.bvcf} --indv {params.normalsample} --recode --recode-INFO-all --out canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}/{params.normalsample}; Canvas.dll Germline-WGS -b {input.normal} -o canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample} -r {params.kmer} -g {params.genome} -f {params.filter} --sample-name={params.normalsample} --sample-b-allele-vcf=canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}/{params.normalsample}.recode.vcf; mv canvas_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample}/CNV.vcf.gz canvas_out/{params.normalsample}+{params.tumorsample}/tumor_CNV.vcf.gz; mv canvas_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}/CNV.vcf.gz canvas_out/{params.normalsample}+{params.tumorsample}/normal_CNV.vcf.gz" \ No newline at end of file diff --git a/Rules/canvas_wgs_tumoronly.rl b/Rules/canvas_wgs_tumoronly.rl index 006fc29..a5c4319 100644 --- a/Rules/canvas_wgs_tumoronly.rl +++ b/Rules/canvas_wgs_tumoronly.rl @@ -3,4 +3,4 @@ rule canvas_wgs_tumoronly: somaticvcf=config['project']['workpath']+"/mutect2_out/{x}.FINALmutect2.vcf", output: vcf="canvas_out/{x}/CNV.vcf.gz", params: genome=config['references'][pfamily]['CANVASGENOME'],tumorsample=lambda wildcards: config['project']['units'][wildcards.x],kmer=config['references'][pfamily]['CANVASKMER'],filter=config['references'][pfamily]['CANVASFILTER'],balleles=config['references'][pfamily]['KNOWNVCF2'],rname="pl:canvas" - shell: "mkdir -p canvas_out; mkdir -p canvas_out/{params.tumorsample}; cp {params.tumorsample}.recal.bai {params.tumorsample}.recal.bam.bai; export COMPlus_gcAllowVeryLargeObjects=1; module load Canvas/1.25; Canvas.dll Somatic-WGS -b {input.tumor} -o canvas_out/{params.tumorsample} -r {params.kmer} -g {params.genome} -f {params.filter} --sample-name={params.tumorsample} --population-b-allele-vcf={params.balleles} --somatic-vcf={input.somaticvcf}" \ No newline at end of file + shell: "mkdir -p canvas_out; mkdir -p canvas_out/{params.tumorsample}; cp {params.tumorsample}.recal.bai {params.tumorsample}.recal.bam.bai; export COMPlus_gcAllowVeryLargeObjects=1; module load Canvas/1.31; Canvas.dll Somatic-WGS -b {input.tumor} -o canvas_out/{params.tumorsample} -r {params.kmer} -g {params.genome} -f {params.filter} --sample-name={params.tumorsample} --population-b-allele-vcf={params.balleles} --somatic-vcf={input.somaticvcf}" \ No newline at end of file diff --git a/Rules/cnvkit_germ.rl b/Rules/cnvkit_germ.rl index bf6fa0d..c62dc66 100755 --- a/Rules/cnvkit_germ.rl +++ b/Rules/cnvkit_germ.rl @@ -3,4 +3,4 @@ rule cnvkit_germ: output: heatmap="cnvkit_out/cnvkit_heatmap.pdf" threads: 12 params: cnvkitgenome=config['references'][pfamily]['CNVKITREF'],rname="pl:cnvkit" - shell: "mkdir -p cnvkit_out; cd cnvkit_out; module load cnvkit/0.8.5; cnvkit.py batch --scatter --method wgs -r {params.cnvkitgenome} -p {threads} ../*.recal.bam; cnvkit.py heatmap -d -o cnvkit_heatmap.pdf *.cns" \ No newline at end of file + shell: "mkdir -p cnvkit_out; cd cnvkit_out; module load cnvkit/0.9.3; cnvkit.py batch --scatter --method wgs -r {params.cnvkitgenome} -p {threads} ../*.recal.bam; cnvkit.py heatmap -d -o cnvkit_heatmap.pdf *.cns" \ No newline at end of file diff --git a/Rules/cnvkit_somatic.rl b/Rules/cnvkit_somatic.rl index ad76882..90cfe91 100755 --- a/Rules/cnvkit_somatic.rl +++ b/Rules/cnvkit_somatic.rl @@ -11,4 +11,4 @@ rule cnvkit_somatic: dir=config['project']['workpath']+"/cnvkit_out/{x}_cnvkit" params: vcfdir=config['project']['workpath']+"/germline_vcfs",tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],access=config['references'][pfamily]['CNVKITACCESS'],targets="cnvkit_targets.bed",antitargets="cnvkit_antitargets.bed",genome=config['references'][pfamily]['CNVKITGENOME'],regions="exome_targets.bed",snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:cnvkit_somatic" threads: 2 - shell: "module load GATK/3.6; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T GenotypeGVCFs -R {params.genome} --annotation InbreedingCoeff --annotation FisherStrand --annotation QualByDepth --annotation ChromosomeCounts --dbsnp {params.snpsites} -o {output.vcf} -nt {threads} --variant {input.normalgvcf} --variant {input.tumorgvcf} -L {params.regions}; module load vcftools; vcftools --vcf {output.vcf} --recode --recode-INFO-all --non-ref-ac-any 2 --remove-indels --max-missing 1 --minGQ 20 --out {params.normalsample}+{params.tumorsample}_filt; mv {params.normalsample}+{params.tumorsample}_filt.recode.vcf {output.filtvcf}; module load cnvkit/0.8.5; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.tumor} {params.antitargets} -q 20 -o {output.dir}/{params.tumorsample}.antitargetcoverage.cnn; cnvkit.py coverage {input.normal} {params.targets} -q 20 -o {output.dir}/{params.normalsample}.targetcoverage.cnn; cnvkit.py coverage {input.normal} {params.antitargets} -q 20 -o {output.dir}/{params.normalsample}.antitargetcoverage.cnn; cnvkit.py reference {output.dir}/{params.normalsample}.targetcoverage.cnn {output.dir}/{params.normalsample}.antitargetcoverage.cnn -f {params.genome} -o {output.dir}/{params.normalsample}.reference.cnn; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {output.dir}/{params.tumorsample}.antitargetcoverage.cnn {output.dir}/{params.normalsample}.reference.cnn -o {output.dir}/{params.tumorsample}.cnr; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr --drop-low-coverage -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 --drop-low-coverage -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns --drop-low-coverage -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr" \ No newline at end of file + shell: "module load GATK/3.6; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T GenotypeGVCFs -R {params.genome} --annotation InbreedingCoeff --annotation FisherStrand --annotation QualByDepth --annotation ChromosomeCounts --dbsnp {params.snpsites} -o {output.vcf} -nt {threads} --variant {input.normalgvcf} --variant {input.tumorgvcf} -L {params.regions}; module load vcftools; vcftools --vcf {output.vcf} --recode --recode-INFO-all --non-ref-ac-any 2 --remove-indels --max-missing 1 --minGQ 20 --out {params.normalsample}+{params.tumorsample}_filt; mv {params.normalsample}+{params.tumorsample}_filt.recode.vcf {output.filtvcf}; module load cnvkit/0.9.3; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.tumor} {params.antitargets} -q 20 -o {output.dir}/{params.tumorsample}.antitargetcoverage.cnn; cnvkit.py coverage {input.normal} {params.targets} -q 20 -o {output.dir}/{params.normalsample}.targetcoverage.cnn; cnvkit.py coverage {input.normal} {params.antitargets} -q 20 -o {output.dir}/{params.normalsample}.antitargetcoverage.cnn; cnvkit.py reference {output.dir}/{params.normalsample}.targetcoverage.cnn {output.dir}/{params.normalsample}.antitargetcoverage.cnn -f {params.genome} -o {output.dir}/{params.normalsample}.reference.cnn; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {output.dir}/{params.tumorsample}.antitargetcoverage.cnn {output.dir}/{params.normalsample}.reference.cnn -o {output.dir}/{params.tumorsample}.cnr; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr --drop-low-coverage -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 --drop-low-coverage -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns --drop-low-coverage -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr" \ No newline at end of file diff --git a/Rules/cnvkit_somatic_tumoronly.rl b/Rules/cnvkit_somatic_tumoronly.rl index 482587a..2f54bcc 100644 --- a/Rules/cnvkit_somatic_tumoronly.rl +++ b/Rules/cnvkit_somatic_tumoronly.rl @@ -7,4 +7,4 @@ rule cnvkit_somatic_tumoronly: dir=config['project']['workpath']+"/cnvkit_out/{x}_cnvkit" params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],access=config['references'][pfamily]['CNVKITACCESS'],targets="cnvkit_targets.bed",antitargets="cnvkit_antitargets.bed",genome=config['references'][pfamily]['CNVKITGENOME'],regions="exome_targets.bed",rname="pl:cnvkit_somatic" threads: 1 - shell: "module load cnvkit/0.8.5; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.tumor} {params.antitargets} -q 20 -o {output.dir}/{params.tumorsample}.antitargetcoverage.cnn; cnvkit.py reference -f {params.genome} -o {output.dir}/{params.tumorsample}.FLATreference.cnn -t {params.targets} -a {params.antitargets}; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {output.dir}/{params.tumorsample}.antitargetcoverage.cnn {output.dir}/{params.tumorsample}.FLATreference.cnn -o {output.dir}/{params.tumorsample}.cnr; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr --drop-low-coverage -i {params.tumorsample} -z -v {input.vcf} -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -z -v {input.vcf} -i {params.tumorsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -i {params.tumorsample} -z -v {input.vcf} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 --drop-low-coverage -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns --drop-low-coverage -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr" \ No newline at end of file + shell: "module load cnvkit/0.9.3; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.tumor} {params.antitargets} -q 20 -o {output.dir}/{params.tumorsample}.antitargetcoverage.cnn; cnvkit.py reference -f {params.genome} -o {output.dir}/{params.tumorsample}.FLATreference.cnn -t {params.targets} -a {params.antitargets}; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {output.dir}/{params.tumorsample}.antitargetcoverage.cnn {output.dir}/{params.tumorsample}.FLATreference.cnn -o {output.dir}/{params.tumorsample}.cnr; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr --drop-low-coverage -i {params.tumorsample} -z -v {input.vcf} -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -z -v {input.vcf} -i {params.tumorsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -i {params.tumorsample} -z -v {input.vcf} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 --drop-low-coverage -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns --drop-low-coverage -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr" \ No newline at end of file diff --git a/Rules/cnvkit_summary.rl b/Rules/cnvkit_summary.rl index 655b268..e767582 100755 --- a/Rules/cnvkit_summary.rl +++ b/Rules/cnvkit_summary.rl @@ -2,4 +2,4 @@ rule cnvkit_summary: input: cnvkit=expand(config['project']['workpath']+"/cnvkit_out/{p}_calls.cns",p=pairs) output: heatmap=config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf" params: rname="pl:cnvkit_summary" - shell: "module load cnvkit/0.8.5; cnvkit.py heatmap -d -o {output.heatmap} cnvkit_out/*.cns; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/cnplot.R cnvkit_out; cd cnvkit_out; perl ../Scripts/summarize_CNVs.pl" \ No newline at end of file + shell: "module load cnvkit/0.9.3; cnvkit.py heatmap -d -o {output.heatmap} cnvkit_out/*.cns; module load R/3.5; Rscript Scripts/cnplot.R cnvkit_out; cd cnvkit_out; perl ../Scripts/summarize_CNVs.pl" \ No newline at end of file diff --git a/Rules/cnvkit_summary_tumoronly.rl b/Rules/cnvkit_summary_tumoronly.rl index d8fb151..3b91154 100644 --- a/Rules/cnvkit_summary_tumoronly.rl +++ b/Rules/cnvkit_summary_tumoronly.rl @@ -2,4 +2,4 @@ rule cnvkit_summary_tumoronly: input: cnvkit=expand(config['project']['workpath']+"/cnvkit_out/{s}_calls.cns",s=samples) output: heatmap=config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf",summary="cnvkit_out/AllCNValteredGenes.txt" params: rname="pl:cnvkit_summary" - shell: "module load cnvkit/0.8.5; cnvkit.py heatmap -d -o {output.heatmap} cnvkit_out/*.cns; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/cnplot.R cnvkit_out; cd cnvkit_out; perl ../Scripts/summarize_CNVs.pl" \ No newline at end of file + shell: "module load cnvkit/0.9.3; cnvkit.py heatmap -d -o {output.heatmap} cnvkit_out/*.cns; module load R/3.5; Rscript Scripts/cnplot.R cnvkit_out; cd cnvkit_out; perl ../Scripts/summarize_CNVs.pl" \ No newline at end of file diff --git a/Rules/cnvkit_wgs_somatic.rl b/Rules/cnvkit_wgs_somatic.rl index 35ba06d..a64e2d6 100644 --- a/Rules/cnvkit_wgs_somatic.rl +++ b/Rules/cnvkit_wgs_somatic.rl @@ -11,4 +11,4 @@ rule cnvkit_wgs_somatic: # theta=config['project']['workpath']+"/cnvkit_out/{x}_thetaIN", params: vcfdir=config['project']['workpath']+"/germline_vcfs",tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],access=config['references'][pfamily]['CNVKITACCESS'],antitargets=config['references'][pfamily]['CNVKITANTITARGETS'],genome=config['references'][pfamily]['CNVKITGENOME'],snpsites=config['references'][pfamily]['SNPSITES'],targets=config['references'][pfamily]['CNVKITWGSTARGETS'],rname="pl:cnvkit" threads: 2 - shell: "module load GATK/3.6; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T GenotypeGVCFs -R {params.genome} --annotation InbreedingCoeff --annotation FisherStrand --annotation QualByDepth --annotation ChromosomeCounts --dbsnp {params.snpsites} -o {output.vcf} -nt {threads} --variant {input.normalgvcf} --variant {input.tumorgvcf}; module load vcftools; vcftools --vcf {output.vcf} --recode --recode-INFO-all --non-ref-ac-any 2 --remove-indels --max-missing 1 --minGQ 20 --out {params.normalsample}+{params.tumorsample}_filt; mv {params.normalsample}+{params.tumorsample}_filt.recode.vcf {output.filtvcf}; module load cnvkit/0.8.5; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -p {threads} -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.normal} {params.targets} -q 20 -p {threads} -o {output.dir}/{params.normalsample}.targetcoverage.cnn; cnvkit.py reference {output.dir}/{params.normalsample}.targetcoverage.cnn {params.antitargets} -f {params.genome} -o {output.dir}/{params.normalsample}.reference.cnn --no-edge; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {params.antitargets} {output.dir}/{params.normalsample}.reference.cnn -o {output.dir}/{params.tumorsample}.cnr --no-edge; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -p {threads} -t 1e-6 -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr" \ No newline at end of file + shell: "module load GATK/3.6; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T GenotypeGVCFs -R {params.genome} --annotation InbreedingCoeff --annotation FisherStrand --annotation QualByDepth --annotation ChromosomeCounts --dbsnp {params.snpsites} -o {output.vcf} -nt {threads} --variant {input.normalgvcf} --variant {input.tumorgvcf}; module load vcftools; vcftools --vcf {output.vcf} --recode --recode-INFO-all --non-ref-ac-any 2 --remove-indels --max-missing 1 --minGQ 20 --out {params.normalsample}+{params.tumorsample}_filt; mv {params.normalsample}+{params.tumorsample}_filt.recode.vcf {output.filtvcf}; module load cnvkit/0.9.3; mkdir -p {output.dir}; cnvkit.py coverage {input.tumor} {params.targets} -q 20 -p {threads} -o {output.dir}/{params.tumorsample}.targetcoverage.cnn; cnvkit.py coverage {input.normal} {params.targets} -q 20 -p {threads} -o {output.dir}/{params.normalsample}.targetcoverage.cnn; cnvkit.py reference {output.dir}/{params.normalsample}.targetcoverage.cnn {params.antitargets} -f {params.genome} -o {output.dir}/{params.normalsample}.reference.cnn --no-edge; cnvkit.py fix {output.dir}/{params.tumorsample}.targetcoverage.cnn {params.antitargets} {output.dir}/{params.normalsample}.reference.cnn -o {output.dir}/{params.tumorsample}.cnr --no-edge; cnvkit.py segment {output.dir}/{params.tumorsample}.cnr -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -p {threads} -t 1e-6 -o {output.dir}/{params.tumorsample}.cns; cnvkit.py scatter {output.dir}/{params.tumorsample}.cnr -s {output.dir}/{params.tumorsample}.cns -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} -o {output.dir}/{params.tumorsample}.png; cnvkit.py call -o {output.calls} -v {output.filtvcf} -i {params.tumorsample} -n {params.normalsample} {output.dir}/{params.tumorsample}.cns; cnvkit.py gainloss -s {output.dir}/{params.tumorsample}.cns -t 0.3 -o {output.gainloss} {output.dir}/{params.tumorsample}.cnr; cnvkit.py segmetrics -s {output.dir}/{params.tumorsample}.cns -o {output.dir}/{params.tumorsample}.segmetrics --mean --median --mode --stdev --sem --mad --mse --iqr --bivar --ci --pi -b 1000 {output.dir}/{params.tumorsample}.cnr" \ No newline at end of file diff --git a/Rules/database_germline.rl b/Rules/database_germline.rl index 0766b5b..63d038d 100755 --- a/Rules/database_germline.rl +++ b/Rules/database_germline.rl @@ -4,4 +4,4 @@ rule database_germline: output: dbase="variants.database", vcf="exome_genotypes.vcf" params: regions=config['references'][pfamily]['REFFLAT'],rname="pl:database" - shell: "unzip -p full_annot.txt.zip > full_annot.txt; gzip exome.relaxedFilter.vcf; module load samtools; bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT]\n' exome.relaxedFilter.vcf.gz > exome_genotypes.vcf; gunzip exome.relaxedFilter.vcf.gz; perl Scripts/make_database.pl {input.vcf} {output.vcf}; sed '1!b;s/#//g' variants.database > temp.database; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/dedupcol.R; echo -n "create table vcf (\"" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\t/" text, "/g' | sed '${s/$/\" text);/}' >> sqlite3.commands; echo ".separator \"\\t\"" >> sqlite3.commands; echo ".import temp.database vcf" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 vcf.db < sqlite3.commands" \ No newline at end of file + shell: "unzip -p full_annot.txt.zip > full_annot.txt; gzip exome.relaxedFilter.vcf; module load samtools; bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT]\n' exome.relaxedFilter.vcf.gz > exome_genotypes.vcf; gunzip exome.relaxedFilter.vcf.gz; perl Scripts/make_database.pl {input.vcf} {output.vcf}; sed '1!b;s/#//g' variants.database > temp.database; module load R/3.5; Rscript Scripts/dedupcol.R; echo -n "create table vcf (\"" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\t/" text, "/g' | sed '${s/$/\" text);/}' >> sqlite3.commands; echo ".separator \"\\t\"" >> sqlite3.commands; echo ".import temp.database vcf" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 vcf.db < sqlite3.commands" \ No newline at end of file diff --git a/Rules/database_somatic.rl b/Rules/database_somatic.rl index cbf5d69..5e3a534 100755 --- a/Rules/database_somatic.rl +++ b/Rules/database_somatic.rl @@ -6,4 +6,4 @@ rule database_somatic: mutectdbase=config['project']['workpath']+"/mutect_out/mutect_variants.database", strelkadbase=config['project']['workpath']+"/strelka_out/strelka_variants.database", params: rname="pl:database" - shell: "cd mutect2_out; sed '1!b;s/#//g' {input.mutect2maf} > temp.database; module load R/3.4.0_gcc-6.2.0; Rscript ../Scripts/dedupcol.R; echo -n \"create table vcf (\\\"\" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\\t/\" text, \"/g' | sed '${{s/$/\\\" text);/}}' >> sqlite3.commands; echo \".separator \\\"\\\\t\\\"\" >> sqlite3.commands; echo \".import temp.database vcf\" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 {output.mutect2dbase} < sqlite3.commands; cd ../mutect_out; sed '1!b;s/#//g' {input.mutectmaf} > temp.database; module load R/3.4.0_gcc-6.2.0; Rscript ../Scripts/dedupcol.R; echo -n \"create table vcf (\\\"\" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\\t/\" text, \"/g' | sed '${{s/$/\\\" text);/}}' >> sqlite3.commands; echo \".separator \\\"\\\\t\\\"\" >> sqlite3.commands; echo \".import temp.database vcf\" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 {output.mutectdbase} < sqlite3.commands; cd ../strelka_out; sed '1!b;s/#//g' {input.strelkamaf} > temp.database; module load R/3.4.0_gcc-6.2.0; Rscript ../Scripts/dedupcol.R; echo -n \"create table vcf (\\\"\" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\\t/\" text, \"/g' | sed '${{s/$/\\\" text);/}}' >> sqlite3.commands; echo \".separator \\\"\\\\t\\\"\" >> sqlite3.commands; echo \".import temp.database vcf\" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 {output.strelkadbase} < sqlite3.commands" \ No newline at end of file + shell: "cd mutect2_out; sed '1!b;s/#//g' {input.mutect2maf} > temp.database; module load R/3.5; Rscript ../Scripts/dedupcol.R; echo -n \"create table vcf (\\\"\" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\\t/\" text, \"/g' | sed '${{s/$/\\\" text);/}}' >> sqlite3.commands; echo \".separator \\\"\\\\t\\\"\" >> sqlite3.commands; echo \".import temp.database vcf\" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 {output.mutect2dbase} < sqlite3.commands; cd ../mutect_out; sed '1!b;s/#//g' {input.mutectmaf} > temp.database; module load R/3.5; Rscript ../Scripts/dedupcol.R; echo -n \"create table vcf (\\\"\" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\\t/\" text, \"/g' | sed '${{s/$/\\\" text);/}}' >> sqlite3.commands; echo \".separator \\\"\\\\t\\\"\" >> sqlite3.commands; echo \".import temp.database vcf\" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 {output.mutectdbase} < sqlite3.commands; cd ../strelka_out; sed '1!b;s/#//g' {input.strelkamaf} > temp.database; module load R/3.5; Rscript ../Scripts/dedupcol.R; echo -n \"create table vcf (\\\"\" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\\t/\" text, \"/g' | sed '${{s/$/\\\" text);/}}' >> sqlite3.commands; echo \".separator \\\"\\\\t\\\"\" >> sqlite3.commands; echo \".import temp.database vcf\" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 {output.strelkadbase} < sqlite3.commands" \ No newline at end of file diff --git a/Rules/database_somatic_tumoronly.rl b/Rules/database_somatic_tumoronly.rl index 3c24d56..e5ab24b 100644 --- a/Rules/database_somatic_tumoronly.rl +++ b/Rules/database_somatic_tumoronly.rl @@ -2,4 +2,4 @@ rule database_somatic_tumoronly: input: mutect2maf=config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_filtered.maf", output: mutect2dbase=config['project']['workpath']+"/mutect2_out/mutect2_variants.database", params: rname="pl:database" - shell: "cd mutect2_out; sed '1!b;s/#//g' {input.mutect2maf} > temp.database; module load R/3.4.0_gcc-6.2.0; Rscript ../Scripts/dedupcol.R; echo -n \"create table vcf (\\\"\" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\\t/\" text, \"/g' | sed '${{s/$/\\\" text);/}}' >> sqlite3.commands; echo \".separator \\\"\\\\t\\\"\" >> sqlite3.commands; echo \".import temp.database vcf\" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 {output.mutect2dbase} < sqlite3.commands" \ No newline at end of file + shell: "cd mutect2_out; sed '1!b;s/#//g' {input.mutect2maf} > temp.database; module load R/3.5; Rscript ../Scripts/dedupcol.R; echo -n \"create table vcf (\\\"\" > sqlite3.commands; sed -n 1p temp.database | sed 's/#//g' | sed 's/\\t/\" text, \"/g' | sed '${{s/$/\\\" text);/}}' >> sqlite3.commands; echo \".separator \\\"\\\\t\\\"\" >> sqlite3.commands; echo \".import temp.database vcf\" >> sqlite3.commands; tail -n +2 temp.database > temp.temp.database; mv temp.temp.database temp.database; sqlite3 {output.mutect2dbase} < sqlite3.commands" \ No newline at end of file diff --git a/Rules/fusioncatcher.rl b/Rules/fusioncatcher.rl index a20ccf0..9905df4 100644 --- a/Rules/fusioncatcher.rl +++ b/Rules/fusioncatcher.rl @@ -3,4 +3,4 @@ rule fusioncatcher: output: "fusioncatcher/{x}/final-list_candidate-fusion-genes.txt" params: data=config['references'][pfamily]['FUSCATCHDAT'],configfile=config['references'][pfamily]['FUSCATCHDAT'],rname='fusioncatcher',sample="{x}" threads: 16 - shell: "module load fusioncatcher/0.99.7b; mkdir -p fusioncatcher/{params.sample}; fusioncatcher -i {input.file1},{input.file2} -o fusioncatcher/{params.sample} -d {params.data} --threads {threads}" \ No newline at end of file + shell: "module load fusioncatcher/1.00; mkdir -p fusioncatcher/{params.sample}; fusioncatcher -i {input.file1},{input.file2} -o fusioncatcher/{params.sample} -d {params.data} --threads {threads}" diff --git a/Rules/fusioninsp_fuscatch.rl b/Rules/fusioninsp_fuscatch.rl index 6e11bda..28fb9f8 100644 --- a/Rules/fusioninsp_fuscatch.rl +++ b/Rules/fusioninsp_fuscatch.rl @@ -3,4 +3,4 @@ rule fusioninsp_fuscatch: output: "fusioncatcher/fusioninspector/{x}/{x}.fusion_predictions.final" params: rname='fusioninsp',sample="{x}",ref=config['project']['annotation'],starlib=config['references'][pfamily]['STARFUSIONLIB'] threads: 8 - shell: "module load fusioninspector/1.0.1; module load python/2.7; mkdir -p fusioncatcher/fusioninspector/{params.sample}; perl Scripts/make_fusioninspector_input.pl {params.sample} {params.ref}; FusionInspector --fusions fusioncatcher/fusioninspector/{params.sample}/{params.sample}_fusionInspector.input --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir fusioncatcher/fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV" \ No newline at end of file + shell: "module load fusioninspector/1.1.0; module load python/2.7; mkdir -p fusioncatcher/fusioninspector/{params.sample}; perl Scripts/make_fusioninspector_input.pl {params.sample} {params.ref}; FusionInspector --fusions fusioncatcher/fusioninspector/{params.sample}/{params.sample}_fusionInspector.input --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir fusioncatcher/fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV" \ No newline at end of file diff --git a/Rules/fusioninsp_starfus.rl b/Rules/fusioninsp_starfus.rl index 8e4d2e0..e8d579a 100644 --- a/Rules/fusioninsp_starfus.rl +++ b/Rules/fusioninsp_starfus.rl @@ -2,4 +2,4 @@ rule rule fusioninsp_starfus: input: fusions="starfusion/{x}/star-fusion.fusion_candidates.final",file1="{x}.R1.trimmed.fastq.gz",file2="{x}.R2.trimmed.fastq.gz" output: "starfusion/fusioninspector/{x}/{x}.fusion_predictions.final" params: rname='fusioninsp',sample="{x}",starlib=config['references'][pfamily]['STARFUSIONLIB'] - shell: "module load fusioninspector/1.0.1; module load python/2.7; mkdir -p starfusion/fusioninspector/{params.sample}; FusionInspector --fusions {input.fusions} --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir starfusion/fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV" \ No newline at end of file + shell: "module load fusioninspector/1.1.0; module load python/2.7; mkdir -p starfusion/fusioninspector/{params.sample}; FusionInspector --fusions {input.fusions} --genome_lib {params.starlib} --left_fq {input.file1} --right_fq {input.file2} --out_dir starfusion/fusioninspector/{params.sample} --out_prefix {params.sample} --prep_for_IGV" \ No newline at end of file diff --git a/Rules/gatk.haplotype.caller.rl b/Rules/gatk.haplotype.caller.rl index 5a800fc..5aeae5b 100755 --- a/Rules/gatk.haplotype.caller.rl +++ b/Rules/gatk.haplotype.caller.rl @@ -3,6 +3,6 @@ rule gatk_haplotype_caller: output:"{x}.g.vcf" params: gres="lscratch:100",gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:hapcall" threads: 4 - shell: "{params.gatk} -T HaplotypeCaller -R {params.genome} -I {input} --read_filter BadCigar --emitRefConfidence GVCF --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest --variant_index_type LINEAR --dbsnp {params.snpsites} --variant_index_parameter 128000 -nct {threads} -o {output[0]}" + shell: "module load GATK/3.8-0; java -Xmx64g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T HaplotypeCaller -R {params.genome} -I {input} --read_filter BadCigar --emitRefConfidence GVCF --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest --variant_index_type LINEAR --dbsnp {params.snpsites} --variant_index_parameter 128000 -nct {threads} -o {output[0]}" diff --git a/Rules/gatk.merge.mutect2.chrom.rl b/Rules/gatk.merge.mutect2.chrom.rl index 4e75139..91202ec 100755 --- a/Rules/gatk.merge.mutect2.chrom.rl +++ b/Rules/gatk.merge.mutect2.chrom.rl @@ -35,8 +35,8 @@ if config['project']['annotation'] == "hg19": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" + params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" elif config['project']['annotation'] == "hg38": rule gatk_merge_mutect2_chrom: @@ -75,8 +75,8 @@ elif config['project']['annotation'] == "hg38": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" + params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" elif config['project']['annotation'] == "mm10": @@ -113,5 +113,5 @@ elif config['project']['annotation'] == "mm10": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" \ No newline at end of file + params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" \ No newline at end of file diff --git a/Rules/gatk.merge.mutect2.chrom.tumoronly.rl b/Rules/gatk.merge.mutect2.chrom.tumoronly.rl index e27de76..a300197 100644 --- a/Rules/gatk.merge.mutect2.chrom.tumoronly.rl +++ b/Rules/gatk.merge.mutect2.chrom.tumoronly.rl @@ -35,8 +35,8 @@ if config['project']['annotation'] == "hg19": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets=config['references'][pfamily]['REFFLAT'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" + params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets=config['references'][pfamily]['REFFLAT'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" elif config['project']['annotation'] == "hg38": rule gatk_merge_mutect2_chrom: @@ -75,8 +75,8 @@ elif config['project']['annotation'] == "hg38": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets=config['references'][pfamily]['REFFLAT'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" + params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets=config['references'][pfamily]['REFFLAT'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" elif config['project']['annotation'] == "mm10": @@ -113,5 +113,5 @@ elif config['project']['annotation'] == "mm10": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets=config['references'][pfamily]['REFFLAT'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" \ No newline at end of file + params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets=config['references'][pfamily]['REFFLAT'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -L {input.targets} -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -interval {input.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" \ No newline at end of file diff --git a/Rules/gatk.merge.wgs.mutect2.chrom.rl b/Rules/gatk.merge.wgs.mutect2.chrom.rl index 0239eaa..6b6e521 100644 --- a/Rules/gatk.merge.wgs.mutect2.chrom.rl +++ b/Rules/gatk.merge.wgs.mutect2.chrom.rl @@ -34,8 +34,8 @@ if config['project']['annotation'] == "hg19": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" + params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" else: @@ -71,5 +71,5 @@ else: snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" \ No newline at end of file + params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.filtered} > {output.snpeffout}; sed -ie 's/NORMAL/{params.normalsample}/g' {output.filtered}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" \ No newline at end of file diff --git a/Rules/gatk.merge.wgs.mutect2.chrom.tumoronly.rl b/Rules/gatk.merge.wgs.mutect2.chrom.tumoronly.rl index 5f47009..2b10773 100644 --- a/Rules/gatk.merge.wgs.mutect2.chrom.tumoronly.rl +++ b/Rules/gatk.merge.wgs.mutect2.chrom.tumoronly.rl @@ -34,8 +34,8 @@ if config['project']['annotation'] == "hg19": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" + params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" elif config['project']['annotation'] == "hg38": rule gatk_merge_mutect2_chrom: @@ -73,8 +73,8 @@ elif config['project']['annotation'] == "hg38": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" + params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcf20} --variant {input.vcf21} --variant {input.vcf22} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" elif config['project']['annotation'] == "mm10": @@ -110,5 +110,5 @@ elif config['project']['annotation'] == "mm10": snpeffout=config['project']['workpath']+"/mutect2_out/{x}.snpeff.out", csvstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.csv", htmlstats=config['project']['workpath']+"/mutect2_out/{x}.mutect2.stats.html", - params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:merge.mutect2" - shell: "module load GATK/3.7; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" \ No newline at end of file + params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:merge.mutect2" + shell: "module load GATK/3.8-0; GATK -m 64G CombineVariants -R {params.genome} --filteredrecordsmergetype KEEP_UNCONDITIONAL --assumeIdenticalSamples -o {output.vcf} --variant {input.vcf1} --variant {input.vcf2} --variant {input.vcf3} --variant {input.vcf4} --variant {input.vcf5} --variant {input.vcf6} --variant {input.vcf7} --variant {input.vcf8} --variant {input.vcf9} --variant {input.vcf10} --variant {input.vcf11} --variant {input.vcf12} --variant {input.vcf13} --variant {input.vcf14} --variant {input.vcf15} --variant {input.vcf16} --variant {input.vcf17} --variant {input.vcf18} --variant {input.vcf19} --variant {input.vcfX} --variant {input.vcfY}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType SNP --excludeFiltered -o {output.snps}; GATK -m 120G SelectVariants -R {params.genome} --variant {output.vcf} -selectType INDEL --excludeFiltered -o {output.indels}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.snps} --filterExpression \"FS > 60.0 || SOR > 3.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\" --filterName \"my_snp_filter\" -o {output.flagsnps}; GATK -m 48G VariantFiltration -R {params.genome} --variant {output.indels} --filterExpression \"FS > 200.0 || SOR > 10.0 || ReadPosRankSum < -20.0\" --filterName \"my_indel_filter\" -o {output.flagindels}; GATK -m 48G CombineVariants -R {params.genome} --variant {output.flagsnps} --variant {output.flagindels} -o {output.flagged} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL --genotypemergeoption UNSORTED; GATK -m 48G SelectVariants -R {params.genome} --variant {output.flagged} --excludeFiltered -o {output.filtered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} {output.filtered} > {output.snpeffout}; sed -ie 's/TUMOR/{params.tumorsample}/g' {output.filtered}" \ No newline at end of file diff --git a/Rules/gatk.mutect2.rl b/Rules/gatk.mutect2.rl index 0e0a8e2..26cf680 100755 --- a/Rules/gatk.mutect2.rl +++ b/Rules/gatk.mutect2.rl @@ -5,7 +5,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_1.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_1" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 1 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 1 -o {output.vcf}" rule gatk_mutect2_2: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -13,7 +13,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_2.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_2" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 2 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 2 -o {output.vcf}" rule gatk_mutect2_3: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -21,7 +21,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_3.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_3" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 3 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 3 -o {output.vcf}" rule gatk_mutect2_4: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -29,7 +29,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_4.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_4" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 4 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 4 -o {output.vcf}" rule gatk_mutect2_5: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -37,7 +37,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_5.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_5" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 5 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 5 -o {output.vcf}" rule gatk_mutect2_6: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -45,7 +45,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_6.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_6" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 6 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 6 -o {output.vcf}" rule gatk_mutect2_7: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -53,7 +53,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_7.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_7" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 7 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 7 -o {output.vcf}" rule gatk_mutect2_8: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -61,7 +61,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_8.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_8" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 8 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 8 -o {output.vcf}" rule gatk_mutect2_9: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -69,7 +69,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_9.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_9" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 9 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 9 -o {output.vcf}" rule gatk_mutect2_10: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -77,7 +77,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_10.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_10" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 10 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 10 -o {output.vcf}" rule gatk_mutect2_11: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -85,7 +85,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_11.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_11" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 11 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 11 -o {output.vcf}" rule gatk_mutect2_12: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -93,7 +93,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_12.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_12" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 12 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 12 -o {output.vcf}" rule gatk_mutect2_13: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -101,7 +101,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_13.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_13" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 13 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 13 -o {output.vcf}" rule gatk_mutect2_14: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -109,7 +109,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_14.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_14" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 14 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 14 -o {output.vcf}" rule gatk_mutect2_15: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -117,7 +117,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_15.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_15" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 15 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 15 -o {output.vcf}" rule gatk_mutect2_16: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -125,7 +125,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_16.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_16" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 16 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 16 -o {output.vcf}" rule gatk_mutect2_17: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -133,7 +133,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_17.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_17" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 17 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 17 -o {output.vcf}" rule gatk_mutect2_18: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -141,7 +141,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_18.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_18" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 18 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 18 -o {output.vcf}" rule gatk_mutect2_19: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -149,7 +149,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_19.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_19" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 19 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 19 -o {output.vcf}" rule gatk_mutect2_20: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -157,7 +157,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_20.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_20" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 20 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 20 -o {output.vcf}" rule gatk_mutect2_21: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -165,7 +165,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_21.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_21" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 21 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 21 -o {output.vcf}" rule gatk_mutect2_22: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -173,7 +173,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_22.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_22" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 22 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 22 -o {output.vcf}" rule gatk_mutect2_X: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -181,7 +181,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_X.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_X" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L X -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L X -o {output.vcf}" rule gatk_mutect2_Y: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -189,7 +189,7 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_Y.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_Y" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L Y -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L Y -o {output.vcf}" elif config['project']['annotation'] == "hg38": @@ -199,7 +199,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_1.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_1" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr1 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr1 -o {output.vcf}" rule gatk_mutect2_2: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -207,7 +207,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_2.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_2" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr2 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr2 -o {output.vcf}" rule gatk_mutect2_3: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -215,7 +215,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_3.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_3" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr3 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr3 -o {output.vcf}" rule gatk_mutect2_4: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -223,7 +223,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_4.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_4" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr4 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr4 -o {output.vcf}" rule gatk_mutect2_5: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -231,7 +231,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_5.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_5" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr5 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr5 -o {output.vcf}" rule gatk_mutect2_6: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -239,7 +239,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_6.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_6" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr6 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr6 -o {output.vcf}" rule gatk_mutect2_7: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -247,7 +247,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_7.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_7" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr7 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr7 -o {output.vcf}" rule gatk_mutect2_8: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -255,7 +255,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_8.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_8" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr8 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr8 -o {output.vcf}" rule gatk_mutect2_9: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -263,7 +263,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_9.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_9" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr9 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr9 -o {output.vcf}" rule gatk_mutect2_10: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -271,7 +271,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_10.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_10" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr10 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr10 -o {output.vcf}" rule gatk_mutect2_11: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -279,7 +279,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_11.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_11" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr11 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr11 -o {output.vcf}" rule gatk_mutect2_12: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -287,7 +287,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_12.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_12" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr12 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr12 -o {output.vcf}" rule gatk_mutect2_13: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -295,7 +295,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_13.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_13" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr13 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr13 -o {output.vcf}" rule gatk_mutect2_14: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -303,7 +303,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_14.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_14" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr14 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr14 -o {output.vcf}" rule gatk_mutect2_15: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -311,7 +311,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_15.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_15" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr15 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr15 -o {output.vcf}" rule gatk_mutect2_16: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -319,7 +319,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_16.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_16" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr16 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr16 -o {output.vcf}" rule gatk_mutect2_17: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -327,7 +327,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_17.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_17" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr17 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr17 -o {output.vcf}" rule gatk_mutect2_18: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -335,7 +335,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_18.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_18" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr18 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr18 -o {output.vcf}" rule gatk_mutect2_19: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -343,7 +343,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_19.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_19" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr19 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr19 -o {output.vcf}" rule gatk_mutect2_20: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -351,7 +351,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_20.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_20" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr20 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr20 -o {output.vcf}" rule gatk_mutect2_21: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -359,7 +359,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_21.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_21" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr21 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr21 -o {output.vcf}" rule gatk_mutect2_22: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -367,7 +367,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_22.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_22" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr22 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr22 -o {output.vcf}" rule gatk_mutect2_X: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -375,7 +375,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_X.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_X" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrX -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrX -o {output.vcf}" rule gatk_mutect2_Y: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -383,7 +383,7 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_Y.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_Y" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrY -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrY -o {output.vcf}" elif config['project']['annotation'] == "mm10": @@ -393,7 +393,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_1.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr1" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr1 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr1 -o {output.vcf}" rule gatk_mutect2_2: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -401,7 +401,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_2.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr2" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr2 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr2 -o {output.vcf}" rule gatk_mutect2_3: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -409,7 +409,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_3.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr3" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr3 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr3 -o {output.vcf}" rule gatk_mutect2_4: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -417,7 +417,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_4.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr4" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr4 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr4 -o {output.vcf}" rule gatk_mutect2_5: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -425,7 +425,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_5.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr5" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr5 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr5 -o {output.vcf}" rule gatk_mutect2_6: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -433,7 +433,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_6.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr6" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr6 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr6 -o {output.vcf}" rule gatk_mutect2_7: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -441,7 +441,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_7.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr7" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr7 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr7 -o {output.vcf}" rule gatk_mutect2_8: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -449,7 +449,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_8.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr8" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr8 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr8 -o {output.vcf}" rule gatk_mutect2_9: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -457,7 +457,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_9.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr9" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr9 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr9 -o {output.vcf}" rule gatk_mutect2_10: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -465,7 +465,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_10.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr10" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr10 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr10 -o {output.vcf}" rule gatk_mutect2_11: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -473,7 +473,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_11.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr11" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr11 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr11 -o {output.vcf}" rule gatk_mutect2_12: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -481,7 +481,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_12.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr12" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr12 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr12 -o {output.vcf}" rule gatk_mutect2_13: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -489,7 +489,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_13.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr13" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr13 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr13 -o {output.vcf}" rule gatk_mutect2_14: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -497,7 +497,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_14.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr14" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr14 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr14 -o {output.vcf}" rule gatk_mutect2_15: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -505,7 +505,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_15.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr15" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr15 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr15 -o {output.vcf}" rule gatk_mutect2_16: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -513,7 +513,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_16.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr16" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr16 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr16 -o {output.vcf}" rule gatk_mutect2_17: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -521,7 +521,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_17.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr17" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr17 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr17 -o {output.vcf}" rule gatk_mutect2_18: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -529,7 +529,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_18.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr18" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr18 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr18 -o {output.vcf}" rule gatk_mutect2_19: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -537,7 +537,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_19.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr19" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr19 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr19 -o {output.vcf}" rule gatk_mutect2_X: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -545,7 +545,7 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_X.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chrX" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrX -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrX -o {output.vcf}" rule gatk_mutect2_Y: input: normal=ancient(lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam"), @@ -553,4 +553,4 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_Y.vcf" params: pon=config['references'][pfamily]['PON'],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chrY" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrY -o {output.vcf}" \ No newline at end of file + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input.tumor} -I:normal {input.normal} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrY -o {output.vcf}" \ No newline at end of file diff --git a/Rules/gatk.mutect2.tumoronly.rl b/Rules/gatk.mutect2.tumoronly.rl index 949c55b..659e780 100644 --- a/Rules/gatk.mutect2.tumoronly.rl +++ b/Rules/gatk.mutect2.tumoronly.rl @@ -4,168 +4,168 @@ if config['project']['annotation'] == "hg19": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_1.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_1" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 1 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 1 -o {output.vcf}" rule gatk_mutect2_tumoronly_2: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_2.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_2" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 2 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 2 -o {output.vcf}" rule gatk_mutect2_tumoronly_3: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_3.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_3" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 3 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 3 -o {output.vcf}" rule gatk_mutect2_tumoronly_4: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_4.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_4" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 4 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 4 -o {output.vcf}" rule gatk_mutect2_tumoronly_5: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_5.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_5" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 5 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 5 -o {output.vcf}" rule gatk_mutect2_tumoronly_6: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_6.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_6" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 6 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 6 -o {output.vcf}" rule gatk_mutect2_tumoronly_7: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_7.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_7" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 7 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 7 -o {output.vcf}" rule gatk_mutect2_tumoronly_8: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_8.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_8" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 8 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 8 -o {output.vcf}" rule gatk_mutect2_tumoronly_9: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_9.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_9" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 9 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 9 -o {output.vcf}" rule gatk_mutect2_tumoronly_10: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_10.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_10" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 10 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 10 -o {output.vcf}" rule gatk_mutect2_tumoronly_11: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_11.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_11" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 11 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 11 -o {output.vcf}" rule gatk_mutect2_tumoronly_12: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_12.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_12" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 12 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 12 -o {output.vcf}" rule gatk_mutect2_tumoronly_13: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_13.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_13" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 13 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 13 -o {output.vcf}" rule gatk_mutect2_tumoronly_14: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_14.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_14" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 14 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 14 -o {output.vcf}" rule gatk_mutect2_tumoronly_15: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_15.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_15" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 15 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 15 -o {output.vcf}" rule gatk_mutect2_tumoronly_16: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_16.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_16" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 16 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 16 -o {output.vcf}" rule gatk_mutect2_tumoronly_17: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_17.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_17" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 17 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 17 -o {output.vcf}" rule gatk_mutect2_tumoronly_18: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_18.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_18" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 18 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 18 -o {output.vcf}" rule gatk_mutect2_tumoronly_19: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_19.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_19" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 19 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 19 -o {output.vcf}" rule gatk_mutect2_tumoronly_20: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_20.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_20" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 20 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 20 -o {output.vcf}" rule gatk_mutect2_tumoronly_21: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_21.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_21" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 21 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 21 -o {output.vcf}" rule gatk_mutect2_tumoronly_22: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_22.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_22" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 22 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L 22 -o {output.vcf}" rule gatk_mutect2_tumoronly_X: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_X.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_X" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L X -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L X -o {output.vcf}" rule gatk_mutect2_tumoronly_Y: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_Y.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_Y" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L Y -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L Y -o {output.vcf}" elif config['project']['annotation'] == "hg38": @@ -174,168 +174,168 @@ elif config['project']['annotation'] == "hg38": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_1.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_1" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr1 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr1 -o {output.vcf}" rule gatk_mutect2_tumoronly_2: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_2.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_2" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr2 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr2 -o {output.vcf}" rule gatk_mutect2_tumoronly_3: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_3.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_3" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr3 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr3 -o {output.vcf}" rule gatk_mutect2_tumoronly_4: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_4.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_4" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr4 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr4 -o {output.vcf}" rule gatk_mutect2_tumoronly_5: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_5.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_5" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr5 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr5 -o {output.vcf}" rule gatk_mutect2_tumoronly_6: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_6.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_6" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr6 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr6 -o {output.vcf}" rule gatk_mutect2_tumoronly_7: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_7.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_7" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr7 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr7 -o {output.vcf}" rule gatk_mutect2_tumoronly_8: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_8.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_8" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr8 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr8 -o {output.vcf}" rule gatk_mutect2_tumoronly_9: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_9.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_9" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr9 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr9 -o {output.vcf}" rule gatk_mutect2_tumoronly_10: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_10.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_10" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr10 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr10 -o {output.vcf}" rule gatk_mutect2_tumoronly_11: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_11.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_11" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr11 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr11 -o {output.vcf}" rule gatk_mutect2_tumoronly_12: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_12.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_12" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr12 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr12 -o {output.vcf}" rule gatk_mutect2_tumoronly_13: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_13.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_13" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr13 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr13 -o {output.vcf}" rule gatk_mutect2_tumoronly_14: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_14.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_14" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr14 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr14 -o {output.vcf}" rule gatk_mutect2_tumoronly_15: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_15.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_15" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr15 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr15 -o {output.vcf}" rule gatk_mutect2_tumoronly_16: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_16.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_16" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr16 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr16 -o {output.vcf}" rule gatk_mutect2_tumoronly_17: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_17.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_17" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr17 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr17 -o {output.vcf}" rule gatk_mutect2_tumoronly_18: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_18.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_18" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr18 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr18 -o {output.vcf}" rule gatk_mutect2_tumoronly_19: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_19.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_19" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr19 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr19 -o {output.vcf}" rule gatk_mutect2_tumoronly_20: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_20.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_20" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr20 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr20 -o {output.vcf}" rule gatk_mutect2_tumoronly_21: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_21.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_21" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr21 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr21 -o {output.vcf}" rule gatk_mutect2_tumoronly_22: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_22.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_22" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr22 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr22 -o {output.vcf}" rule gatk_mutect2_tumoronly_X: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_X.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_X" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrX -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrX -o {output.vcf}" rule gatk_mutect2_tumoronly_Y: input: "{x}.recal.bam" output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_Y.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_Y" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrY -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrY -o {output.vcf}" elif config['project']['annotation'] == "mm10": @@ -344,144 +344,144 @@ elif config['project']['annotation'] == "mm10": output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_1.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr1" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr1 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr1 -o {output.vcf}" rule gatk_mutect2_tumoronly_2: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_2.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr2" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr2 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr2 -o {output.vcf}" rule gatk_mutect2_tumoronly_3: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_3.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr3" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr3 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr3 -o {output.vcf}" rule gatk_mutect2_tumoronly_4: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_4.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr4" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr4 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr4 -o {output.vcf}" rule gatk_mutect2_tumoronly_5: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_5.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr5" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr5 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr5 -o {output.vcf}" rule gatk_mutect2_tumoronly_6: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_6.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr6" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr6 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr6 -o {output.vcf}" rule gatk_mutect2_tumoronly_7: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_7.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr7" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr7 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr7 -o {output.vcf}" rule gatk_mutect2_tumoronly_8: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_8.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr8" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr8 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr8 -o {output.vcf}" rule gatk_mutect2_tumoronly_9: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_9.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr9" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr9 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr9 -o {output.vcf}" rule gatk_mutect2_tumoronly_10: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_10.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr10" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr10 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr10 -o {output.vcf}" rule gatk_mutect2_tumoronly_11: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_11.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr11" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr11 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr11 -o {output.vcf}" rule gatk_mutect2_tumoronly_12: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_12.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr12" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr12 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr12 -o {output.vcf}" rule gatk_mutect2_tumoronly_13: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_13.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr13" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr13 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr13 -o {output.vcf}" rule gatk_mutect2_tumoronly_14: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_14.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr14" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr14 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr14 -o {output.vcf}" rule gatk_mutect2_tumoronly_15: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_15.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr15" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr15 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr15 -o {output.vcf}" rule gatk_mutect2_tumoronly_16: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_16.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr16" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr16 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr16 -o {output.vcf}" rule gatk_mutect2_tumoronly_17: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_17.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr17" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr17 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr17 -o {output.vcf}" rule gatk_mutect2_tumoronly_18: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_18.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr18" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr18 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr18 -o {output.vcf}" rule gatk_mutect2_tumoronly_19: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_19.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chr19" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr19 -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chr19 -o {output.vcf}" rule gatk_mutect2_tumoronly_X: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_X.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chrX" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrX -o {output.vcf}" + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrX -o {output.vcf}" rule gatk_mutect2_tumoronly_Y: input: "{x}.recal.bam", output: vcf=config['project']['workpath']+"/mutect2_out/chrom_files/{x}_Y.vcf" params: pon=config['references'][pfamily]['PON'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['MUTECTVARIANTS'],targets=ancient("exome_targets.bed"),rname="pl:mutect2_chrY" threads: 2 - shell: "module load GATK/3.7; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrY -o {output.vcf}" \ No newline at end of file + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T MuTect2 -R {params.genome} -I:tumor {input} -PON {params.pon} -G Standard --read_filter BadCigar --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest {params.knowns} -L chrY -o {output.vcf}" \ No newline at end of file diff --git a/Rules/gatk.realign.2.rl b/Rules/gatk.realign.2.rl index 03a2aa1..98c8e21 100755 --- a/Rules/gatk.realign.2.rl +++ b/Rules/gatk.realign.2.rl @@ -8,8 +8,8 @@ rule gatk_realign2: sam=config['bin'][pfamily]['SAMTOOLS'], picard3=config['bin'][pfamily]['PICARD3'], indelsites=config['references'][pfamily]['INDELSITES'],rname="pl:realign" - shell: "module load novocraft/3.02.10;{params.novosort} -t /scratch -s -i -o {output} {input};{params.sam} index {input};{params.gatk} -T RealignerTargetCreator -I {input} -R {params.genome} -known {params.indelsites} -o {output.int}; {params.gatk} -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} -o {output.re}" + shell: "module load novocraft/3.08.02;{params.novosort} -t /scratch -s -i -o {output} {input};{params.sam} index {input};{params.gatk} -T RealignerTargetCreator -I {input} -R {params.genome} -known {params.indelsites} -o {output.int}; {params.gatk} -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} -o {output.re}" # shell: "{params.sam} index {input}; {params.sam} faidx {params.genome}; {params.gatk} -T RealignerTargetCreator -I {input} -R {params.genome} -known {params.indelsites} -o {output.int}; {params.gatk} -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} -o {output.re}" params: threads: 1 - shell: "module load novocraft/3.02.10;{params.novosort} -t /scratch -s -i -o {output} {input};" + shell: "module load novocraft/3.08.02;{params.novosort} -t /scratch -s -i -o {output} {input};" diff --git a/Rules/gatk.realign.2.rl.bak b/Rules/gatk.realign.2.rl.bak index 7230a98..6b61fef 100755 --- a/Rules/gatk.realign.2.rl.bak +++ b/Rules/gatk.realign.2.rl.bak @@ -8,8 +8,8 @@ rule gatk_realign2: sam=config['bin']['SAMTOOLS'], picard3=config['bin']['PICARD3'], indelsites=config['references']['INDELSITES'],rname="pl:realign" - shell: "module load novocraft/3.02.10;{params.novosort} -t /scratch -s -i -o {output} {input};{params.sam} index {input};{params.gatk} -T RealignerTargetCreator -I {input} -R {params.genome} -known {params.indelsites} -o {output.int}; {params.gatk} -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} -o {output.re}" + shell: "module load novocraft/3.08.02;{params.novosort} -t /scratch -s -i -o {output} {input};{params.sam} index {input};{params.gatk} -T RealignerTargetCreator -I {input} -R {params.genome} -known {params.indelsites} -o {output.int}; {params.gatk} -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} -o {output.re}" # shell: "{params.sam} index {input}; {params.sam} faidx {params.genome}; {params.gatk} -T RealignerTargetCreator -I {input} -R {params.genome} -known {params.indelsites} -o {output.int}; {params.gatk} -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} -o {output.re}" params: threads: 1 - shell: "module load novocraft/3.02.10;{params.novosort} -t /scratch -s -i -o {output} {input};" + shell: "module load novocraft/3.08.02;{params.novosort} -t /scratch -s -i -o {output} {input};" diff --git a/Rules/gatk.realign.rl b/Rules/gatk.realign.rl index 282c4bc..6113946 100755 --- a/Rules/gatk.realign.rl +++ b/Rules/gatk.realign.rl @@ -7,4 +7,4 @@ rule gatk_realign: sam=config['bin'][pfamily]['SAMTOOLS'], picard3=config['bin'][pfamily]['PICARD3'], knownindels=config['references'][pfamily]['KNOWNINDELS'],rname="pl:realign" - shell: "{params.sam} index {input};module load GATK/3.5-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T RealignerTargetCreator -I {input} -R {params.genome} {params.knownindels} -o {output.int}; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T IndelRealigner -R {params.genome} -I {input} -targetIntervals {output.int} {params.knownindels} -o {output.re}" \ No newline at end of file + shell: "module load samtools/1.8; samtools index {input}; module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T RealignerTargetCreator -I {input} -R {params.genome} {params.knownindels} -o {output.int}; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T IndelRealigner -R {params.genome} -I {input} --use_jdk_inflater --use_jdk_deflater -targetIntervals {output.int} {params.knownindels} -o {output.re}" \ No newline at end of file diff --git a/Rules/gatk.recal.rl b/Rules/gatk.recal.rl index 9bdf5d2..dd261f1 100755 --- a/Rules/gatk.recal.rl +++ b/Rules/gatk.recal.rl @@ -4,4 +4,4 @@ rule gatk_recal: re=temp("{x}_recal_data.bam.grp") params: gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],knowns=config['references'][pfamily]['KNOWNRECAL'],rname="pl:recal" threads: 32 - shell: "module load GATK/3.5-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T BaseRecalibrator -I {input} -R {params.genome} {params.knowns} -nct {threads} -o {output.re}; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T PrintReads -R {params.genome} -nct 8 -I {input} -BQSR {output.re} -o {output.bam}" \ No newline at end of file + shell: "module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T BaseRecalibrator -I {input} -R {params.genome} {params.knowns} -nct {threads} -o {output.re}; module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T PrintReads -R {params.genome} -nct 8 -I {input} --use_jdk_inflater --use_jdk_deflater -BQSR {output.re} -o {output.bam}" \ No newline at end of file diff --git a/Rules/gatk_select_variants.rl b/Rules/gatk_select_variants.rl index ebe3537..39ced4a 100755 --- a/Rules/gatk_select_variants.rl +++ b/Rules/gatk_select_variants.rl @@ -6,4 +6,4 @@ rule gatk_select_variants: htmlstats="sample_vcfs/{x}.stats.html", bed="sample_vcfs/{x}.snpeff.bed" params: sample=lambda wildcards: config['project']['units'][wildcards.x],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets="exome_targets.bed",snpeff=config['bin'][pfamily]['SNPEFF'],effgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:extract" - shell: "{params.gatk} -T SelectVariants -R {params.genome} -V {input.vcf} -sn {params.sample} -env -o {output.vcf}; {params.snpeff} -v -c {params.effconfig} -o bed -csvStats {output.csvstats} -stats {output.htmlstats} {params.effgenome} {output.vcf} > {output.bed}" \ No newline at end of file + shell: "{params.gatk} -T SelectVariants -R {params.genome} -V {input.vcf} -sn {params.sample} -env -o {output.vcf}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v -c {params.effconfig} -o bed -csvStats {output.csvstats} -stats {output.htmlstats} {params.effgenome} {output.vcf} > {output.bed}" \ No newline at end of file diff --git a/Rules/initialqcrnaseq.snakefile b/Rules/initialqcrnaseq.snakefile old mode 100755 new mode 100644 index f8e5eee..07b8fcb --- a/Rules/initialqcrnaseq.snakefile +++ b/Rules/initialqcrnaseq.snakefile @@ -91,7 +91,6 @@ fastqc {input} -t {threads} -o {output}; trimmomaticver=config['bin'][pfamily]['tool_versions']['TRIMMOMATICVER'], cutadaptver=config['bin'][pfamily]['tool_versions']['CUTADAPTVER'], parallelver=config['bin'][pfamily]['tool_versions']['PARALLELVER'], - pigzver=config['bin'][pfamily]['tool_versions']['PIGZVER'], fastawithadaptersetc=config['bin'][pfamily]['tool_parameters']['FASTAWITHADAPTERSETC'], fastawithadaptersetd=config['bin'][pfamily]['tool_parameters']['FASTAWITHADAPTERSETD'], seedmismatches=config['bin'][pfamily]['tool_parameters']['SEEDMISMATCHES'], @@ -112,7 +111,6 @@ java -classpath $TRIMMOJAR org.usadellab.trimmomatic.TrimmomaticPE -threads {t elif [ {trim_method} -eq 2 ];then module load {params.cutadaptver}; module load {params.parallelver}; -module load {params.pigzver}; if [ ! -e /lscratch/$SLURM_JOBID ]; then mkdir /lscratch/$SLURM_JOBID ;fi cd /lscratch/$SLURM_JOBID sample=`echo {input.file1}|awk -F "/" '{{print $NF}}'|awk -F ".R1.fastq" '{{print $1}}'` @@ -380,7 +378,6 @@ fastqc {input} -t {threads} -o {output}; trimmomaticver=config['bin'][pfamily]['tool_versions']['TRIMMOMATICVER'], cutadaptver=config['bin'][pfamily]['tool_versions']['CUTADAPTVER'], parallelver=config['bin'][pfamily]['tool_versions']['PARALLELVER'], - pigzver=config['bin'][pfamily]['tool_versions']['PIGZVER'], fastawithadaptersetc=config['bin'][pfamily]['tool_parameters']['FASTAWITHADAPTERSETC'], fastawithadaptersetd=config['bin'][pfamily]['tool_parameters']['FASTAWITHADAPTERSETD'], seedmismatches=config['bin'][pfamily]['tool_parameters']['SEEDMISMATCHES'], @@ -401,7 +398,6 @@ java -classpath $TRIMMOJAR org.usadellab.trimmomatic.TrimmomaticSE -threads {t elif [ {trim_method} -eq 2 ];then module load {params.cutadaptver}; module load {params.parallelver}; -module load {params.pigzver}; if [ ! -e /lscratch/$SLURM_JOBID ]; then mkdir /lscratch/$SLURM_JOBID ;fi cd /lscratch/$SLURM_JOBID sample=`echo {input.file1}|awk -F "/" '{{print $NF}}'|awk -F ".R1.fastq" '{{print $1}}'` @@ -616,8 +612,8 @@ rule picard: picardver=config['bin'][pfamily]['tool_versions']['PICARDVER'], shell: """ module load {params.picardver}; -java -Xmx110g -jar $PICARDJARPATH/AddOrReplaceReadGroups.jar INPUT={input.file1} OUTPUT=/lscratch/$SLURM_JOBID/{params.sampleName}.star_rg_added.sorted.bam TMP_DIR=/lscratch/$SLURM_JOBID RGID=id RGLB=library RGPL=illumina RGPU=machine RGSM=sample; -java -Xmx110g -jar $PICARDJARPATH/MarkDuplicates.jar INPUT=/lscratch/$SLURM_JOBID/{params.sampleName}.star_rg_added.sorted.bam OUTPUT=/lscratch/$SLURM_JOBID/{params.sampleName}.star_rg_added.sorted.dmark.bam TMP_DIR=/lscratch/$SLURM_JOBID CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT METRICS_FILE={output.outstar3}; +java -Xmx110g -jar $PICARDJARPATH/picard.jar AddOrReplaceReadGroups I={input.file1} O=/lscratch/$SLURM_JOBID/{params.sampleName}.star_rg_added.sorted.bam TMP_DIR=/lscratch/$SLURM_JOBID RGID=id RGLB=library RGPL=illumina RGPU=machine RGSM=sample; +java -Xmx110g -jar $PICARDJARPATH/picard.jar MarkDuplicates I=/lscratch/$SLURM_JOBID/{params.sampleName}.star_rg_added.sorted.bam O=/lscratch/$SLURM_JOBID/{params.sampleName}.star_rg_added.sorted.dmark.bam TMP_DIR=/lscratch/$SLURM_JOBID CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT METRICS_FILE={output.outstar3}; mv /lscratch/$SLURM_JOBID/{params.sampleName}.star_rg_added.sorted.dmark.bam {output.outstar2}; mv /lscratch/$SLURM_JOBID/{params.sampleName}.star_rg_added.sorted.dmark.bai {output.outstar2b}; """ @@ -651,9 +647,9 @@ rule stats: rrnalist=config['references'][pfamily]['RRNALIST'], picardstrand=config['bin'][pfamily]['PICARDSTRAND'] shell: """ -module load R/3.4.0_gcc-6.2.0; +module load R/3.5; module load {params.picardver}; -java -Xmx110g -jar $PICARDJARPATH/CollectRnaSeqMetrics.jar REF_FLAT={params.refflat} INPUT={input.file1} OUTPUT={output.outstar1} RIBOSOMAL_INTERVALS={params.rrnalist} STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND TMP_DIR=/lscratch/$SLURM_JOBID VALIDATION_STRINGENCY=SILENT; +java -Xmx110g -jar $PICARDJARPATH/picard.jar CollectRnaSeqMetrics REF_FLAT={params.refflat} I={input.file1} O={output.outstar1} RIBOSOMAL_INTERVALS={params.rrnalist} STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND TMP_DIR=/lscratch/$SLURM_JOBID VALIDATION_STRINGENCY=SILENT; module load {params.samtoolsver}; samtools flagstat {input.file1} > {output.outstar2}; module load python/3.5; @@ -706,18 +702,23 @@ rule rnaseq_multiqc: input: expand(join(workpath,rseqc_dir,"{name}.Rdist.info"),name=samples), expand(join(workpath,"FQscreen","{name}_R1_001_trim_paired_screen.png"),name=samples), + #expand(join(workpath,"FQscreen","{name}_R1_001_trim_paired_screen.txt"),name=samples), expand(join(workpath,log_dir,"{name}.flagstat.concord.txt"),name=samples), expand(join(workpath,log_dir,"{name}.RnaSeqMetrics.txt"),name=samples), + expand(join(workpath,log_dir,"{name}.star.duplic"),name=samples), expand(join(workpath,preseq_dir,"{name}.ccurve"),name=samples), output: join(workpath,"Reports","multiqc_report.html") params: rname="pl:multiqc", + logsdir=join(workpath,log_dir), outdir=join(workpath,"Reports"), multiqcver=config['bin'][pfamily]['tool_versions']['MULTIQCVER'], qcconfig=config['bin'][pfamily]['CONFMULTIQC'] threads: 1 shell: """ +sed -i 's/MarkDuplicates/picard.sam.MarkDuplicates/g' {params.logsdir}/*.star.duplic +sed -i 's/CollectRnaSeqMetrics/picard.analysis.CollectRnaSeqMetrics/g' {params.logsdir}/*.RnaSeqMetrics.txt module load {params.multiqcver} cd {params.outdir} multiqc -f -c {params.qcconfig} --interactive -e cutadapt -d ../ @@ -772,3 +773,5 @@ cd {rseqc_dir} infer_experiment.py -r {params.bedref} -i {input.file1} > {output.out1} read_distribution.py -i {input.file1} -r {params.bedref} > {output.out4} """ + + diff --git a/Rules/maftools.rl b/Rules/maftools.rl index 4c0b48d..20cabf4 100644 --- a/Rules/maftools.rl +++ b/Rules/maftools.rl @@ -15,4 +15,4 @@ rule maftools: strelkasummary=config['project']['workpath']+"/strelka_out/strelka_maf_summary.pdf", strelkaoncoprint=config['project']['workpath']+"/strelka_out/strelka_oncoplot.pdf", params: dir=config['project']['workpath'],rname="pl:maftools" - shell: "cat mutect2_out/oncotator_out/*.maf > mutect2_out/oncotator_out/mutect2_variants.maf; cat mutect_out/oncotator_out/*.maf > mutect_out/oncotator_out/mutect_variants.maf; cat strelka_out/oncotator_out/*.maf > strelka_out/oncotator_out/strelka_variants.maf; perl Scripts/prep_mafs.pl mutect2_out/oncotator_out/mutect2_variants.maf mutect2; perl Scripts/prep_mafs.pl mutect_out/oncotator_out/mutect_variants.maf mutect; perl Scripts/prep_mafs.pl strelka_out/oncotator_out/strelka_variants.maf strelka; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ mutect2_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary {output.mutect2oncoprint}; Rscript Scripts/maftools.R {params.dir}/mutect_out/oncotator_out/ mutect_filtered.maf {params.dir}/mutect_out/mutect_maf_summary {output.mutectoncoprint}; Rscript Scripts/maftools.R {params.dir}/strelka_out/oncotator_out/ strelka_filtered.maf {params.dir}/strelka_out/strelka_maf_summary {output.strelkaoncoprint}" \ No newline at end of file + shell: "cat mutect2_out/oncotator_out/*.maf > mutect2_out/oncotator_out/mutect2_variants.maf; cat mutect_out/oncotator_out/*.maf > mutect_out/oncotator_out/mutect_variants.maf; cat strelka_out/oncotator_out/*.maf > strelka_out/oncotator_out/strelka_variants.maf; perl Scripts/prep_mafs.pl mutect2_out/oncotator_out/mutect2_variants.maf mutect2; perl Scripts/prep_mafs.pl mutect_out/oncotator_out/mutect_variants.maf mutect; perl Scripts/prep_mafs.pl strelka_out/oncotator_out/strelka_variants.maf strelka; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ mutect2_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.mutect2oncoprint}; Rscript Scripts/maftools.R {params.dir}/mutect_out/oncotator_out/ mutect_filtered.maf {params.dir}/mutect_out/mutect_maf_summary.pdf {output.mutectoncoprint}; Rscript Scripts/maftools.R {params.dir}/strelka_out/oncotator_out/ strelka_filtered.maf {params.dir}/strelka_out/strelka_maf_summary.pdf {output.strelkaoncoprint}" \ No newline at end of file diff --git a/Rules/maftools_tumoronly.rl b/Rules/maftools_tumoronly.rl index 7d57efe..07d500f 100644 --- a/Rules/maftools_tumoronly.rl +++ b/Rules/maftools_tumoronly.rl @@ -4,4 +4,4 @@ rule maftools_tumoronly: mutect2summary=config['project']['workpath']+"/mutect2_out/mutect2_maf_summary.pdf", mutect2oncoprint=config['project']['workpath']+"/mutect2_out/mutect2_oncoplot.pdf", params: dir=config['project']['workpath'],rname="pl:maftools" - shell: "cat mutect2_out/oncotator_out/*.maf > mutect2_out/oncotator_out/mutect2_variants.maf; perl Scripts/prep_mafs.pl mutect2_out/oncotator_out/mutect2_variants.maf mutect2; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ mutect2_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary {output.mutect2oncoprint}" \ No newline at end of file + shell: "cat mutect2_out/oncotator_out/*.maf > mutect2_out/oncotator_out/mutect2_variants.maf; perl Scripts/prep_mafs.pl mutect2_out/oncotator_out/mutect2_variants.maf mutect2; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ mutect2_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.mutect2oncoprint}" \ No newline at end of file diff --git a/Rules/make_target_files.rl b/Rules/make_target_files.rl index a3ed8d0..cd95092 100755 --- a/Rules/make_target_files.rl +++ b/Rules/make_target_files.rl @@ -4,4 +4,4 @@ rule make_target_files: cnvkittargets=config['project']['workpath']+"/cnvkit_targets.bed", cnvkitantitargets=config['project']['workpath']+"/cnvkit_antitargets.bed" params: bed=config['project']['targetspath'],access=config['references'][pfamily]['CNVKITACCESS'],gtf=config['references'][pfamily]['CNVKITANNO'],rname="pl:targets" - shell: "perl Scripts/reformat_bed.pl {params.bed}; module load cnvkit/0.8.5; cnvkit.py target --split --short-names --annotate {params.gtf} -o {output.cnvkittargets} {params.bed}; cnvkit.py antitarget -o {output.cnvkitantitargets} -g {params.access} {params.bed}" \ No newline at end of file + shell: "perl Scripts/reformat_bed.pl {params.bed}; module load cnvkit/0.9.3; cnvkit.py target --split --short-names --annotate {params.gtf} -o {output.cnvkittargets} {params.bed}; cnvkit.py antitarget -o {output.cnvkitantitargets} -g {params.access} {params.bed}" \ No newline at end of file diff --git a/Rules/manta_somatic.rl b/Rules/manta_somatic.rl index 1a98fa4..203dfbe 100755 --- a/Rules/manta_somatic.rl +++ b/Rules/manta_somatic.rl @@ -4,4 +4,4 @@ rule manta_somatic: output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz", params: tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0], gres="lscratch:100",gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:manta_somatic" threads: 8 - shell: "mkdir -p manta_out/{params.normalsample}+{params.tumorsample}; module load manta/1.1.0; module load python/2.7; configManta.py --bam={input.normal} --tumorBam={input.tumor} --referenceFasta {params.genome} --exome --runDir manta_out/{params.normalsample}+{params.tumorsample}; manta_out/{params.normalsample}+{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12" \ No newline at end of file + shell: "mkdir -p manta_out/{params.normalsample}+{params.tumorsample}; module load manta/1.3.0; module load python/2.7; configManta.py --bam={input.normal} --tumorBam={input.tumor} --referenceFasta {params.genome} --exome --runDir manta_out/{params.normalsample}+{params.tumorsample}; manta_out/{params.normalsample}+{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12" \ No newline at end of file diff --git a/Rules/manta_somatic_tumoronly.rl b/Rules/manta_somatic_tumoronly.rl index a6fce4f..6514576 100644 --- a/Rules/manta_somatic_tumoronly.rl +++ b/Rules/manta_somatic_tumoronly.rl @@ -3,4 +3,4 @@ rule manta_somatic_tumoronly: output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz", params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:manta" threads: 8 - shell: "mkdir -p manta_out/{params.tumorsample}; module load manta/1.1.0; module load python/2.7; configManta.py --tumorBam={input.tumor} --referenceFasta {params.genome} --exome --runDir manta_out/{params.tumorsample}; manta_out/{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12" \ No newline at end of file + shell: "mkdir -p manta_out/{params.tumorsample}; module load manta/1.3.0; module load python/2.7; configManta.py --tumorBam={input.tumor} --referenceFasta {params.genome} --exome --runDir manta_out/{params.tumorsample}; manta_out/{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12" \ No newline at end of file diff --git a/Rules/manta_wgs_somatic.rl b/Rules/manta_wgs_somatic.rl index 24792ed..148d6f7 100644 --- a/Rules/manta_wgs_somatic.rl +++ b/Rules/manta_wgs_somatic.rl @@ -4,4 +4,4 @@ rule manta_wgs_somatic: output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz", params: tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],genome=config['references'][pfamily]['GENOME'],rname="pl:manta" threads: 8 - shell: "mkdir -p manta_out/{params.normalsample}+{params.tumorsample}; module load manta/1.1.0; module load python/2.7; configManta.py --bam={input.normal} --tumorBam={input.tumor} --referenceFasta {params.genome} --runDir manta_out/{params.normalsample}+{params.tumorsample}; manta_out/{params.normalsample}+{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12" \ No newline at end of file + shell: "mkdir -p manta_out/{params.normalsample}+{params.tumorsample}; module load manta/1.3.0; module load python/2.7; configManta.py --bam={input.normal} --tumorBam={input.tumor} --referenceFasta {params.genome} --runDir manta_out/{params.normalsample}+{params.tumorsample}; manta_out/{params.normalsample}+{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12" \ No newline at end of file diff --git a/Rules/manta_wgs_somatic_tumoronly.rl b/Rules/manta_wgs_somatic_tumoronly.rl index f23aafd..986f012 100644 --- a/Rules/manta_wgs_somatic_tumoronly.rl +++ b/Rules/manta_wgs_somatic_tumoronly.rl @@ -3,4 +3,4 @@ rule manta_wgs_somatic_tumoronly: output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz", params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],genome=config['references'][pfamily]['GENOME'],rname="pl:manta" threads: 8 - shell: "mkdir -p manta_out/{params.tumorsample}; module load manta/1.1.0; module load python/2.7; configManta.py --tumorBam={input.tumor} --referenceFasta {params.genome} --runDir manta_out/{params.tumorsample}; manta_out/{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12" \ No newline at end of file + shell: "mkdir -p manta_out/{params.tumorsample}; module load manta/1.3.0; module load python/2.7; configManta.py --tumorBam={input.tumor} --referenceFasta {params.genome} --runDir manta_out/{params.tumorsample}; manta_out/{params.tumorsample}/runWorkflow.py -m local -j {threads} -g 12" \ No newline at end of file diff --git a/Rules/multiqc.rl b/Rules/multiqc.rl index 8da842d..190442e 100755 --- a/Rules/multiqc.rl +++ b/Rules/multiqc.rl @@ -3,6 +3,6 @@ rule multiqc: output: "multiqc_report.html" params: fastqc=config['bin'][pfamily]['FASTQC'],adapters=config['references'][pfamily]['fastqc.adapters'],rname="pl:multiqc" threads: 1 - shell: "module load multiqc/1.1; multiqc -f -e featureCounts ." + shell: "module load multiqc/1.4; multiqc -f -e featureCounts ." diff --git a/Rules/multiqc_genomeseq.rl b/Rules/multiqc_genomeseq.rl index cb407a1..bc2a4d3 100755 --- a/Rules/multiqc_genomeseq.rl +++ b/Rules/multiqc_genomeseq.rl @@ -3,6 +3,6 @@ rule multiqc_genomeseq: output: "multiqc_report.html" params: fastqc=config['bin'][pfamily]['FASTQC'],adapters=config['references'][pfamily]['fastqc.adapters'],rname="pl:multiqc_genome" threads: 1 - shell: "module load multiqc/1.1; multiqc -f -e featureCounts ." + shell: "module load multiqc/1.4; multiqc -f -e featureCounts ." diff --git a/Rules/mutect.rl b/Rules/mutect.rl index 6b7a143..d0ea6b5 100755 --- a/Rules/mutect.rl +++ b/Rules/mutect.rl @@ -8,5 +8,5 @@ rule mutect: csvstats=config['project']['workpath']+"/mutect_out/{x}.mutect.stats.csv", htmlstats=config['project']['workpath']+"/mutect_out/{x}.mutect.stats.html", out=config['project']['workpath']+"/mutect_out/{x}.snpeff.out" - params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],targets="exome_targets.bed",knowns=config['references'][pfamily]['MUTECTVARIANTS'],mutect=config['bin'][pfamily]['MUTECT'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['MUTECTGENOME'],cosmic=config['references'][pfamily]['MUTECTCOSMIC'],snp=config['references'][pfamily]['MUTECTSNP'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],rname="pl:mutect" - shell: "{params.mutect} --analysis_type MuTect --reference_sequence {params.genome} --vcf {output.vcf} {params.knowns} --intervals {params.targets} --input_file:normal {input.normal} --input_file:tumor {input.tumor} --out {output.stats} -rf BadCigar; {params.gatk} -T SelectVariants -R {params.genome} --variant {output.vcf} --excludeFiltered -o {output.vcfRename}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -interval {params.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples pairs {output.vcfRename} > {output.out}" \ No newline at end of file + params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],targets="exome_targets.bed",knowns=config['references'][pfamily]['MUTECTVARIANTS'],mutect=config['bin'][pfamily]['MUTECT'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['MUTECTGENOME'],cosmic=config['references'][pfamily]['MUTECTCOSMIC'],snp=config['references'][pfamily]['MUTECTSNP'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:mutect" + shell: "module load muTect/1.1.7; muTect --analysis_type MuTect --reference_sequence {params.genome} --vcf {output.vcf} {params.knowns} --intervals {params.targets} --disable_auto_index_creation_and_locking_when_reading_rods --input_file:normal {input.normal} --input_file:tumor {input.tumor} --out {output.stats} -rf BadCigar; module load GATK/3.8-0; module load java/1.8.0_92; GATK -m 48G SelectVariants -R {params.genome} --variant {output.vcf} --excludeFiltered -o {output.vcfRename}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -interval {params.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples pairs {output.vcfRename} > {output.out}" \ No newline at end of file diff --git a/Rules/novocraft.novoalign.rl b/Rules/novocraft.novoalign.rl index 35c025f..8d2273c 100755 --- a/Rules/novocraft.novoalign.rl +++ b/Rules/novocraft.novoalign.rl @@ -12,7 +12,7 @@ rule novocraft_novoalign: # message: "Executing NovoAlign Rule." threads: 32 version: "1.0" - shell: "module load novocraft/3.02.10; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} | {params.sam} view -bS - > {output.bam};" -# shell: "module load novocraft/3.02.10; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} > {output.sam};" + shell: "module load novocraft/3.08.02; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} | {params.sam} view -bS - > {output.bam};" +# shell: "module load novocraft/3.08.02; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} > {output.sam};" #{params.qcal} {output.qcal} {output.qcal}.qcalreport.pdf; diff --git a/Rules/novocraft.novoalign.rl.bak b/Rules/novocraft.novoalign.rl.bak index 57f99a3..43a06ce 100755 --- a/Rules/novocraft.novoalign.rl.bak +++ b/Rules/novocraft.novoalign.rl.bak @@ -12,7 +12,7 @@ rule novocraft_novoalign: # message: "Executing NovoAlign Rule." threads: 16 version: "1.0" - shell: "module load novocraft/3.02.10; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} | {params.sam} view -bS - > {output.bam};" -# shell: "module load novocraft/3.02.10; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} > {output.sam};" + shell: "module load novocraft/3.08.02; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} | {params.sam} view -bS - > {output.bam};" +# shell: "module load novocraft/3.08.02; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} > {output.sam};" #{params.qcal} {output.qcal} {output.qcal}.qcalreport.pdf; diff --git a/Rules/novocraft.novoalign.rl~ b/Rules/novocraft.novoalign.rl~ index bd2f64f..ce832e7 100755 --- a/Rules/novocraft.novoalign.rl~ +++ b/Rules/novocraft.novoalign.rl~ @@ -12,7 +12,7 @@ rule novocraft_novoalign: # message: "Executing NovoAlign Rule." threads: 16 version: "1.0" - shell: "module load novocraft/3.02.10; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} | {params.sam} view -bS - > {output.bam};" -# shell: "module load novocraft/3.02.10; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} > {output.sam};" + shell: "module load novocraft/3.08.02; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} | {params.sam} view -bS - > {output.bam};" +# shell: "module load novocraft/3.08.02; novoalign -c {threads} -d {params.novoindex} -a {params.adapter1} {params.adapter2} -H 10 -k -K {output.qcal} -i PE 180,50 -o SAM -f {input} > {output.sam};" #{params.qcal} {output.qcal} {output.qcal}.qcalreport.pdf; diff --git a/Rules/novocraft.sort.rl b/Rules/novocraft.sort.rl index e192567..d35665b 100755 --- a/Rules/novocraft.sort.rl +++ b/Rules/novocraft.sort.rl @@ -3,6 +3,6 @@ rule novocraft_sort: output: temp("{x}.sorted.bam") params: novosort=config['bin'][pfamily]['NOVOSORT'],rname="pl:novosort" threads: 8 - shell: "module load novocraft/3.02.10;{params.novosort} -t /scratch -m 100G --threads {threads} -s -i -o {output} {input};" + shell: "module load novocraft/3.08.02; novosort -t /scratch -m 100G --threads {threads} -s -i -o {output} {input};" diff --git a/Rules/novocraft.sort.rl.bak b/Rules/novocraft.sort.rl.bak index 57f6153..3269992 100755 --- a/Rules/novocraft.sort.rl.bak +++ b/Rules/novocraft.sort.rl.bak @@ -3,6 +3,6 @@ rule novocraft_sort: output: temp("{x}.sorted.bam") params: novosort=config['bin']['NOVOSORT'],rname="pl:novosort" threads: 1 - shell: "module load novocraft/3.02.10;{params.novosort} -t /scratch -s -i -o {output} {input};" + shell: "module load novocraft/3.08.02;{params.novosort} -t /scratch -s -i -o {output} {input};" diff --git a/Rules/novocraft.sort.rl~ b/Rules/novocraft.sort.rl~ index 7a37fce..b1b629a 100755 --- a/Rules/novocraft.sort.rl~ +++ b/Rules/novocraft.sort.rl~ @@ -3,6 +3,6 @@ rule novocraft_sort: output: temp("{x}.sorted.bam") params: novosort=config['bin']['NOVOSORT'] threads: 1 - shell: "module load novocraft/3.02.10;{params.novosort} -t /scratch -s -i -o {output} {input};" + shell: "module load novocraft/3.08.02;{params.novosort} -t /scratch -s -i -o {output} {input};" diff --git a/Rules/oncotator.rl b/Rules/oncotator.rl index 9f0daf7..61f70fa 100755 --- a/Rules/oncotator.rl +++ b/Rules/oncotator.rl @@ -4,4 +4,4 @@ rule oncotator: vcf="mutect2_out/{x}.FINAL.vcf" output: maf="mutect2_out/oncotator_out/{x}.maf" params: rname="pl:oncotator" - shell: "module load oncotator/1.9.1.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcf} {output.maf} hg19" \ No newline at end of file + shell: "module load oncotator/1.9.7.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcf} {output.maf} hg19" \ No newline at end of file diff --git a/Rules/oncotator_mutect.rl b/Rules/oncotator_mutect.rl index 585d662..bc2cdc7 100755 --- a/Rules/oncotator_mutect.rl +++ b/Rules/oncotator_mutect.rl @@ -5,7 +5,7 @@ if config['project']['annotation'] == "hg19": vcf=config['project']['workpath']+"/mutect_out/{x}.FINAL.vcf" output: maf=config['project']['workpath']+"/mutect_out/oncotator_out/{x}.maf" params: rname="pl:oncotator_mutect" - shell: "module load oncotator/1.9.1.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcf} {output.maf} hg19" + shell: "module load oncotator/1.9.7.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcf} {output.maf} hg19" elif config['project']['annotation'] == "hg38": rule oncotator_mutect: @@ -14,7 +14,7 @@ elif config['project']['annotation'] == "hg38": vcf=config['project']['workpath']+"/mutect_out/{x}.FINAL.vcf" output: maf=config['project']['workpath']+"/mutect_out/oncotator_out/{x}.maf" params: rname="pl:oncotator_mutect" - shell: "module load oncotator/1.9.1.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcf} {output.maf} hg19" + shell: "module load oncotator/1.9.7.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcf} {output.maf} hg19" elif config['project']['annotation'] == "mm10": rule oncotator_mutect: diff --git a/Rules/oncotator_mutect2.rl b/Rules/oncotator_mutect2.rl index b01e1ef..c521387 100755 --- a/Rules/oncotator_mutect2.rl +++ b/Rules/oncotator_mutect2.rl @@ -5,7 +5,7 @@ if config['project']['annotation'] == "hg19": vcfb=config['project']['workpath']+"/mutect2_out/{x}.FINALmutect2.vcf" output: maf=config['project']['workpath']+"/mutect2_out/oncotator_out/{x}.maf" params: rname="pl:oncotator_mutect2" - shell: "module load oncotator/1.9.1.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcfb} {output.maf} hg19" + shell: "module load oncotator/1.9.7.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcfb} {output.maf} hg19" else: rule oncotator_mutect2: diff --git a/Rules/oncotator_strelka.rl b/Rules/oncotator_strelka.rl index 2c53092..798cb53 100755 --- a/Rules/oncotator_strelka.rl +++ b/Rules/oncotator_strelka.rl @@ -5,7 +5,7 @@ if config['project']['annotation'] == "hg19": vcf=config['project']['workpath']+"/strelka_out/{x}.vcf" output: maf=config['project']['workpath']+"/strelka_out/oncotator_out/{x}.maf" params: rname="pl:oncotator_strelka" - shell: "module load oncotator/1.9.1.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcf} {output.maf} hg19" + shell: "module load oncotator/1.9.7.0; oncotator -v -o TCGAMAF -i VCF -c /fdb/oncotator/oncotator_v1_ds_Jan262015/tx_exact_uniprot_matches.txt -a Tumor_Sample_Barcode:{input.tumor} -a Matched_Norm_Sample_Barcode:{input.normal} --skip-no-alt --db-dir /fdb/oncotator/oncotator_v1_ds_Jan262015 {input.vcf} {output.maf} hg19" else: rule oncotator_strelka: diff --git a/Rules/qualimap.rl b/Rules/qualimap.rl index 768dcb4..ef9a9f0 100755 --- a/Rules/qualimap.rl +++ b/Rules/qualimap.rl @@ -4,4 +4,4 @@ rule qualimap: output: dir="QC/{x}.qualimapReport",txt="QC/{x}.qualimapReport/genome_results.txt" threads: 8 params: qualimap=config['bin'][pfamily]['QUALIMAP'],organism=config['references'][pfamily]['ORGANISM'],regions="exome_targets.bed",rname="pl:qualimap" - shell: "{params.qualimap} bamqc -bam {input.bam} -c gd {params.organism} -ip -outdir {output.dir} -gff {params.regions} -outformat HTML -nt {threads} --skip-duplicated -nw 500 -p NON-STRAND-SPECIFIC" \ No newline at end of file + shell: "module load qualimap/2.2.1; unset DISPLAY; qualimap bamqc -bam {input.bam} -c gd {params.organism} -ip -outdir {output.dir} -gff {params.regions} -outformat HTML -nt {threads} --skip-duplicated -nw 500 -p NON-STRAND-SPECIFIC" \ No newline at end of file diff --git a/Rules/qualimap_wgs.rl b/Rules/qualimap_wgs.rl index 3675990..1241953 100755 --- a/Rules/qualimap_wgs.rl +++ b/Rules/qualimap_wgs.rl @@ -3,4 +3,4 @@ rule qualimap_wgs: output: "QC/{x}.qualimapReport","QC/{x}.qualimapReport/genome_results.txt" threads: 8 params: qualimap=config['bin'][pfamily]['QUALIMAP'],organism=config['references'][pfamily]['ORGANISM'],rname="pl:wgs_qualimap" - shell: "{params.qualimap} bamqc --java-mem-size=96G -bam {input} -c gd {params.organism} -outdir {output} -ip --skip-duplicated -nt {threads} -outformat HTML -nw 500 -p NON-STRAND-SPECIFIC" \ No newline at end of file + shell: "module load qualimap/2.2.1; unset DISPLAY; qualimap bamqc --java-mem-size=96G -bam {input} -c gd {params.organism} -outdir {output} -ip --skip-duplicated -nt {threads} -outformat HTML -nw 500 -p NON-STRAND-SPECIFIC" \ No newline at end of file diff --git a/Rules/rnaseq.snakefile b/Rules/rnaseq.snakefile index 5e3c92b..64f6641 100755 --- a/Rules/rnaseq.snakefile +++ b/Rules/rnaseq.snakefile @@ -382,6 +382,7 @@ rule genejunctioncounts: rscript=join(workpath,"Scripts","genejunctioncounts.R") shell: """ module load {params.rver} +module load bedtools/2.27.1 Rscript {params.rscript} '{params.outdir}' '{input.files}' '{params.geneinfo}' '{params.mincount}' '{params.minsamples}' """ @@ -525,7 +526,7 @@ Rscript pcacall.R '{params.outdir}' '{input.file1}' '{input.file2}' '{params.pro # input: samtab = "sampletable.txt", bam=expand("salmonrun/{name}/quant.sf", name=samples) # output: "salmonrun/sleuth_completed.txt" # params: rname='pl:sleuth',batch='--mem=128g --cpus-per-task=8 --time=10:00:00',dir=config['project']['workpath'],pipeRlib=config['bin'][pfamily]['PIPERLIB'],contrasts=" ".join(config['project']['contrasts']['rcontrasts']),species=config['project']['annotation'] -# shell: "module load R/3.4.0_gcc-6.2.0; Rscript Scripts/sleuth.R '{params.dir}' '{params.pipeRlib}' '{input.samtab}' '{params.contrasts}' '{params.species}'" +# shell: "module load R/3.5; Rscript Scripts/sleuth.R '{params.dir}' '{params.pipeRlib}' '{input.samtab}' '{params.contrasts}' '{params.species}'" rule EBSeq_isoform: input: diff --git a/Rules/rnaseqforfusions.rl b/Rules/rnaseqforfusions.rl index 1e1fc2f..d347796 100644 --- a/Rules/rnaseqforfusions.rl +++ b/Rules/rnaseqforfusions.rl @@ -57,19 +57,19 @@ rule rsemcounts: input: files=expand("{name}.rsem.genes.results", name=samples) output: "RawCountFile_RSEM_genes_filtered.txt" params: rname='pl:genecounts',batch='--mem=8g --time=10:00:00',dir=config['project']['workpath'],mincount=config['project']['MINCOUNTGENES'],minsamples=config['project']['MINSAMPLES'],annotate=config['references'][pfamily]['ANNOTATE'] - shell: "module load R/3.4.0_gcc-6.2.0; Rscript Scripts/rsemcounts.R '{params.dir}' '{input.files}' '{params.mincount}' '{params.minsamples}' '{params.annotate}'" + shell: "module load R/3.5; Rscript Scripts/rsemcounts.R '{params.dir}' '{input.files}' '{params.mincount}' '{params.minsamples}' '{params.annotate}'" rule picard: input: file1= "{name}.p2.Aligned.sortedByCoord.out.bam" output: outstar1=temp("{name}.star_rg_added.sorted.bam"), outstar2=temp("{name}.star_rg_added.sorted.dmark.bam"),outstar3="{name}.star.duplic" params: rname='pl:picard',batch='--mem=24g --time=10:00:00 --gres=lscratch:800'#,picardjarpath=config['bin'][pfamily]['PICARDJARPATH'] - shell: "module load picard/1.119; java -Xmx10g -jar $PICARDJARPATH/AddOrReplaceReadGroups.jar INPUT={input.file1} OUTPUT={output.outstar1} TMP_DIR=/lscratch/$SLURM_JOBID RGID=id RGLB=library RGPL=illumina RGPU=machine RGSM=sample; java -Xmx10g -jar $PICARDJARPATH/MarkDuplicates.jar INPUT={output.outstar1} OUTPUT={output.outstar2} TMP_DIR=/lscratch/$SLURM_JOBID CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT METRICS_FILE={output.outstar3}" + shell: "module load picard/2.17.11; java -Xmx10g -jar $PICARDJARPATH/AddOrReplaceReadGroups.jar INPUT={input.file1} OUTPUT={output.outstar1} TMP_DIR=/lscratch/$SLURM_JOBID RGID=id RGLB=library RGPL=illumina RGPU=machine RGSM=sample; java -Xmx10g -jar $PICARDJARPATH/MarkDuplicates.jar INPUT={output.outstar1} OUTPUT={output.outstar2} TMP_DIR=/lscratch/$SLURM_JOBID CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT METRICS_FILE={output.outstar3}" rule stats: input: file1= "{name}.star_rg_added.sorted.dmark.bam" output: outstar1="{name}.RnaSeqMetrics.txt", outstar2="{name}.flagstat.concord.txt", outstar3="{name}.InsertSizeMetrics.txt", outstar4="{name}.InsertSizeHisto.pdf" params: rname='pl:stats',batch='--mem=24g --time=10:00:00 --gres=lscratch:800',refflat=config['references'][pfamily]['REFFLAT'],rrnalist=config['references'][pfamily]['RRNALIST'],picardstrand=config['bin'][pfamily]['PICARDSTRAND'] - shell: "module load R/3.4.0_gcc-6.2.0;module load picard/1.119; java -Xmx10g -jar $PICARDJARPATH/CollectRnaSeqMetrics.jar REF_FLAT={params.refflat} INPUT={input.file1} OUTPUT={output.outstar1} RIBOSOMAL_INTERVALS={params.rrnalist} STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND TMP_DIR=/lscratch/$SLURM_JOBID VALIDATION_STRINGENCY=SILENT; java -Xmx10g -jar $PICARDJARPATH/CollectInsertSizeMetrics.jar INPUT={input.file1} OUTPUT={output.outstar3} HISTOGRAM_FILE={output.outstar4} MINIMUM_PCT=0.5 TMP_DIR=/lscratch/$SLURM_JOBID ;module load samtools; samtools flagstat {input.file1} > {output.outstar2}; module load python; python Scripts/bam_count_concord_stats.py {input.file1} >> {output.outstar2} " + shell: "module load R/3.5;module load picard/2.17.11; java -Xmx10g -jar $PICARDJARPATH/CollectRnaSeqMetrics.jar REF_FLAT={params.refflat} INPUT={input.file1} OUTPUT={output.outstar1} RIBOSOMAL_INTERVALS={params.rrnalist} STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND TMP_DIR=/lscratch/$SLURM_JOBID VALIDATION_STRINGENCY=SILENT; java -Xmx10g -jar $PICARDJARPATH/CollectInsertSizeMetrics.jar INPUT={input.file1} OUTPUT={output.outstar3} HISTOGRAM_FILE={output.outstar4} MINIMUM_PCT=0.5 TMP_DIR=/lscratch/$SLURM_JOBID ;module load samtools; samtools flagstat {input.file1} > {output.outstar2}; module load python; python Scripts/bam_count_concord_stats.py {input.file1} >> {output.outstar2} " rule prernaseqc: input: expand("{name}.star_rg_added.sorted.dmark.bam", name=samples) @@ -91,7 +91,7 @@ rule rnaseqc: priority: 2 params: rname='pl:rnaseqc',batch='--mem=24g --time=48:00:00',rrnalist=config['references'][pfamily]['RRNALIST'],gtffile=config['references'][pfamily]['GTFFILE'],genomefile=config['references'][pfamily]['GENOMEFILE'] shell: """ - module load bwa/0.7.15 + module load bwa/0.7.17 var="{params.rrnalist}" if [ $var == "-" ]; then java -jar /usr/local/apps/rnaseqc/1.1.8/RNA-SeQC_v1.1.8.jar -n 1000 -s {input} -t {params.gtffile} -r {params.genomefile} -o {output} @@ -130,22 +130,22 @@ rule rseqc: # input: files=expand("{name}.star.count.txt", name=samples) # output: "RawCountFile_genes_filtered.txt" # params: rname='pl:genecounts',batch='--mem=8g --time=10:00:00',dir=config['project']['workpath'],mincount=config['project']['MINCOUNTGENES'],minsamples=config['project']['MINSAMPLES'],annotate=config['references'][pfamily]['ANNOTATE'] -# shell: "module load R/3.4.0_gcc-6.2.0; Rscript Scripts/genecounts.R '{params.dir}' '{input.files}' '{params.mincount}' '{params.minsamples}' '{params.annotate}'" +# shell: "module load R/3.5; Rscript Scripts/genecounts.R '{params.dir}' '{input.files}' '{params.mincount}' '{params.minsamples}' '{params.annotate}'" #rule junctioncounts: # input: files=expand("{name}.p2.SJ.out.tab", name=samples) # output: "RawCountFile_junctions_filtered.txt" # params: rname='pl:junctioncounts',batch='--mem=8g --time=10:00:00',dir=config['project']['workpath'],mincount=config['project']['MINCOUNTJUNCTIONS'],minsamples=config['project']['MINSAMPLES'] -# shell: "module load R/3.4.0_gcc-6.2.0; Rscript Scripts/junctioncounts.R '{params.dir}' '{input.files}' '{params.mincount}' '{params.minsamples}'" +# shell: "module load R/3.5; Rscript Scripts/junctioncounts.R '{params.dir}' '{input.files}' '{params.mincount}' '{params.minsamples}'" #rule genejunctioncounts: # input: files=expand("{name}.p2.SJ.out.tab", name=samples) # output: "RawCountFile_Subread_genejunctions_filtered.txt" # params: rname='pl:genejunctions',batch='--mem=8g --time=10:00:00',dir=config['project']['workpath'],geneinfo=config['references'][pfamily]['GENEINFO'],mincount=config['project']['MINCOUNTGENEJUNCTIONS'],minsamples=config['project']['MINSAMPLES'] -# shell: "module load R/3.4.0_gcc-6.2.0; Rscript Scripts/genejunctioncounts.R '{params.dir}' '{input.files}' '{params.geneinfo}' '{params.mincount}' '{params.minsamples}'" +# shell: "module load R/3.5; Rscript Scripts/genejunctioncounts.R '{params.dir}' '{input.files}' '{params.geneinfo}' '{params.mincount}' '{params.minsamples}'" #rule joincounts: # input: files=expand("{name}.star.count.overlap.txt", name=samples),files2=expand("{name}.p2.ReadsPerGene.out.tab", name=samples) # output: "RawCountFileOverlap.txt","RawCountFileStar.txt" # params: rname='pl:junctioncounts',batch='--mem=8g --time=10:00:00',dir=config['project']['workpath'],starstrandcol=config['bin'][pfamily]['STARSTRANDCOL'] -# shell: "module load R/3.4.0_gcc-6.2.0; Rscript Scripts/joincounts.R '{params.dir}' '{input.files}' '{input.files2}' '{params.starstrandcol}'" \ No newline at end of file +# shell: "module load R/3.5; Rscript Scripts/joincounts.R '{params.dir}' '{input.files}' '{input.files2}' '{params.starstrandcol}'" diff --git a/Rules/scrnaseq.snakefile b/Rules/scrnaseq.snakefile index 47ba91f..d79de01 100644 --- a/Rules/scrnaseq.snakefile +++ b/Rules/scrnaseq.snakefile @@ -35,16 +35,16 @@ rule cellranger: rule scrna_initial: params: rname='pl:scrnainit',batch='--partition=largemem --cpus-per-task=32 --mem=1000g --time=48:00:00',countspath=config['project']['COUNTSPATH'],refer=config['project']['annotation'],dir=config['project']['workpath'],projDesc=config['project']['description'],projectId=config['project']['id'] output: "scrna_initial.html", "{projectId}_seurat_object.rds".format(projectId=config['project']['id']) - shell: "cp Scripts/scrna_initial.Rmd {params.dir}/; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/scrna_initial_call.R '{params.dir}' '{params.countspath}/{params.refer}' '{params.refer}' '{params.projectId}' '{params.projDesc}'" + shell: "cp Scripts/scrna_initial.Rmd {params.dir}/; module load R/3.5; Rscript Scripts/scrna_initial_call.R '{params.dir}' '{params.countspath}/{params.refer}' '{params.refer}' '{params.projectId}' '{params.projDesc}'" rule scrna_jackstraw: params: rname='pl:scrnajackstraw',batch='--partition=largemem --cpus-per-task=32 --mem=1000g --time=48:00:00',dir=config['project']['workpath'],projDesc=config['project']['description'],projectId=config['project']['id'] input: so="{projectId}_seurat_object.rds".format(projectId=config['project']['id']) output: "scrna_jackstraw.html" - shell: "cp Scripts/scrna_jackstraw.Rmd {params.dir}/; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/scrna_jackstraw_call.R '{params.dir}' '{input.so}' '{params.projectId}' '{params.projDesc}'" + shell: "cp Scripts/scrna_jackstraw.Rmd {params.dir}/; module load R/3.5; Rscript Scripts/scrna_jackstraw_call.R '{params.dir}' '{input.so}' '{params.projectId}' '{params.projDesc}'" rule scrna_cluster: params: rname='pl:scrnacluster',batch='--partition=largemem --cpus-per-task=32 --mem=1000g --time=48:00:00',dir=config['project']['workpath'],pcs=config['project']['PCS'],resolution=config['project']['RESOLUTION'],projDesc=config['project']['description'],projectId=config['project']['id'] input: so="{projectId}_seurat_object.rds".format(projectId=config['project']['id']) output: "scrna_cluster_{pcs}_{resolution}.html".format(pcs=config['project']['PCS'],resolution=config['project']['RESOLUTION']) - shell: "cp Scripts/scrna_cluster.Rmd {params.dir}/; module load R/3.4.0_gcc-6.2.0; Rscript Scripts/scrna_cluster_call.R '{params.dir}' '{input.so}' '{params.pcs}' '{params.resolution}' '{params.projectId}' '{params.projDesc}'" \ No newline at end of file + shell: "cp Scripts/scrna_cluster.Rmd {params.dir}/; module load R/3.5; Rscript Scripts/scrna_cluster_call.R '{params.dir}' '{input.so}' '{params.pcs}' '{params.resolution}' '{params.projectId}' '{params.projDesc}'" \ No newline at end of file diff --git a/Rules/snpeff.rl b/Rules/snpeff.rl index 7c0d6fc..99f23ec 100755 --- a/Rules/snpeff.rl +++ b/Rules/snpeff.rl @@ -7,4 +7,4 @@ rule snpeff: strict="exome.strictFilter.snpeff.vcf", relax="exome.relaxedFilter.snpeff.vcf" params: snpeff=config['bin'][pfamily]['SNPEFF'],genome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:snpeff" - run: shell("{params.snpeff} -v -canon -c {params.effconfig} -csvStats snpeff.stats.csv -stats snpeff.stats.html {params.genome} {input.vcf} > {output.vcf}; {params.snpeff} -v -canon -c {params.effconfig} -csvStats snpeff_strictFilter.stats.csv -stats snpeff_strictFilter.stats.html {params.genome} {input.strict} > {output.strict}; {params.snpeff} -v -canon -c {params.effconfig} -csvStats snpeff_relaxFilter.stats.csv -stats snpeff_relaxFilter.stats.html {params.genome} {input.relax} > {output.relax}") \ No newline at end of file + run: shell("module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v -canon -c {params.effconfig} -csvStats snpeff.stats.csv -stats snpeff.stats.html {params.genome} {input.vcf} > {output.vcf}; java -Xmx12g -jar $SNPEFF_JAR -v -canon -c {params.effconfig} -csvStats snpeff_strictFilter.stats.csv -stats snpeff_strictFilter.stats.html {params.genome} {input.strict} > {output.strict}; java -Xmx12g -jar $SNPEFF_JAR -v -canon -c {params.effconfig} -csvStats snpeff_relaxFilter.stats.csv -stats snpeff_relaxFilter.stats.html {params.genome} {input.relax} > {output.relax}") \ No newline at end of file diff --git a/Rules/strelka.rl b/Rules/strelka.rl index dcd701a..01e8dd5 100755 --- a/Rules/strelka.rl +++ b/Rules/strelka.rl @@ -10,6 +10,6 @@ rule strelka: htmlstats=config['project']['workpath']+"/strelka_out/{x}.strelka.stats.html", out=config['project']['workpath']+"/strelka_out/{x}.snpeff.out", names=temp(config['project']['workpath']+"/strelka_out/{x}.samples"), - params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets="exome_targets.bed",snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:strelka_calls" + params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],targets="exome_targets.bed",snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:strelka_calls" threads: 4 - shell: "module load strelka/2.7.1; module load python; configureStrelkaSomaticWorkflow.py --ref={params.genome} --tumor={params.dir}/{input.tumor} --normal={params.dir}/{input.normal} --runDir={output.outdir} --exome; cd {output.outdir}; ./runWorkflow.py -m local -j {threads}; {params.gatk} -T CombineVariants -R {params.genome} --variant results/variants/somatic.snvs.vcf.gz --variant results/variants/somatic.indels.vcf.gz -L {params.dir}/{params.targets} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL -o {output.vcf}; {params.gatk} -T SelectVariants -R {params.genome} --variant {output.vcf} --excludeFiltered -o {output.vcffiltered}; cd {params.dir}/strelka_out; module load samtools/1.5; echo $'NORMAL {params.normalsample}\nTUMOR {params.tumorsample}' > {output.names}; bcftools reheader -o {output.final} -s {output.names} {output.vcffiltered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -interval {params.dir}/{params.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.final} > {output.out}" \ No newline at end of file + shell: "module load strelka/2.9.0; module load python; configureStrelkaSomaticWorkflow.py --ref={params.genome} --tumor={params.dir}/{input.tumor} --normal={params.dir}/{input.normal} --runDir={output.outdir} --exome; cd {output.outdir}; ./runWorkflow.py -m local -j {threads}; {params.gatk} -T CombineVariants -R {params.genome} --variant results/variants/somatic.snvs.vcf.gz --variant results/variants/somatic.indels.vcf.gz -L {params.dir}/{params.targets} --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL -o {output.vcf}; {params.gatk} -T SelectVariants -R {params.genome} --variant {output.vcf} --excludeFiltered -o {output.vcffiltered}; cd {params.dir}/strelka_out; module load samtools/1.6; echo $'NORMAL {params.normalsample}\nTUMOR {params.tumorsample}' > {output.names}; bcftools reheader -o {output.final} -s {output.names} {output.vcffiltered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -interval {params.dir}/{params.targets} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.final} > {output.out}" \ No newline at end of file diff --git a/Rules/theta.rl b/Rules/theta.rl index 28254b4..0a15b8a 100755 --- a/Rules/theta.rl +++ b/Rules/theta.rl @@ -6,4 +6,4 @@ rule theta: output: infile=config['project']['workpath']+"/theta_out/{x}/{x}_thetaIN", # sampdir=config['project']['workpath']+"/theta_out/{x}" threads: 1 - shell: "mkdir -p {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}; module load theta/0.7-7-g8f93e6c; module load cnvkit/0.8.5; cd {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}; cnvkit.py export theta -i {params.tumorsample} -n {params.normalsample} -v {params.workdir}/cnvkit_out/{params.normalsample}+{params.tumorsample}_filtGermpairs.vcf -o {params.normalsample}+{params.tumorsample}_thetaIN {params.workdir}/cnvkit_out/{params.normalsample}+{params.tumorsample}_cnvkit/{params.tumorsample}.cns; RunTHetA {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}+{params.tumorsample}_thetaIN --TUMOR_FILE {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample}.tumor.snp_formatted.txt --NORMAL_FILE {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample}.normal.snp_formatted.txt --MIN_FRAC 0.0001 --NUM_PROCESSES {threads} --OUTPUT_PREFIX {params.tumorsample} --DIR {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample} --BAF" \ No newline at end of file + shell: "mkdir -p {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}; module load theta/0.7-7-g8f93e6c; module load cnvkit/0.9.3; cd {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}; cnvkit.py export theta -i {params.tumorsample} -n {params.normalsample} -v {params.workdir}/cnvkit_out/{params.normalsample}+{params.tumorsample}_filtGermpairs.vcf -o {params.normalsample}+{params.tumorsample}_thetaIN {params.workdir}/cnvkit_out/{params.normalsample}+{params.tumorsample}_cnvkit/{params.tumorsample}.cns; RunTHetA {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}/{params.normalsample}+{params.tumorsample}_thetaIN --TUMOR_FILE {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample}.tumor.snp_formatted.txt --NORMAL_FILE {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample}/{params.tumorsample}.normal.snp_formatted.txt --MIN_FRAC 0.0001 --NUM_PROCESSES {threads} --OUTPUT_PREFIX {params.tumorsample} --DIR {params.workdir}/theta_out/{params.normalsample}+{params.tumorsample} --BAF" \ No newline at end of file diff --git a/Rules/vcf2maf.rl b/Rules/vcf2maf.rl index 0f89146..adf7175 100644 --- a/Rules/vcf2maf.rl +++ b/Rules/vcf2maf.rl @@ -5,7 +5,7 @@ rule vcf2maf_mutect: output: maf=config['project']['workpath']+"/mutect_out/oncotator_out/{x}.maf", vcf=temp("mutect_out/{x}.FINAL.vep.vcf"), params: genome=config['references'][pfamily]['VEPGENOME'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],build=config['references'][pfamily]['VEPBUILD'],species=config['references'][pfamily]['VEPSPECIES'],filtervcf=config['references'][pfamily]['VEPFILTERVCF'],rname="pl:vcf2maf" - shell: "module load vcf2maf/1.6.12; module load samtools/1.5; module load VEP/88; vcf2maf.pl --input-vcf {input.vcf} --output-maf {output.maf} --vep-path $VEP_HOME --vep-data $VEPCACHEDIR --ref-fasta {params.genome} --filter-vcf {params.filtervcf} --vep-forks 2 --vcf-tumor-id {params.tumorsample} --vcf-normal-id {params.normalsample} --tumor-id {params.tumorsample} --normal-id {params.normalsample} --ncbi-build {params.build} --species {params.species}" + shell: "module load vcf2maf/1.6.16; module load VEP/92; vcf2maf.pl --input-vcf {input.vcf} --output-maf {output.maf} --vep-path $VEP_HOME --vep-data $VEPCACHEDIR --ref-fasta {params.genome} --filter-vcf {params.filtervcf} --vep-forks 2 --vcf-tumor-id {params.tumorsample} --vcf-normal-id {params.normalsample} --tumor-id {params.tumorsample} --normal-id {params.normalsample} --ncbi-build {params.build} --species {params.species}" rule vcf2maf_mutect2: input: normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam", @@ -14,7 +14,7 @@ rule vcf2maf_mutect2: output: maf=config['project']['workpath']+"/mutect2_out/oncotator_out/{x}.maf", vcf=temp("mutect2_out/{x}.FINALmutect2.vep.vcf"), params: genome=config['references'][pfamily]['VEPGENOME'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],build=config['references'][pfamily]['VEPBUILD'],species=config['references'][pfamily]['VEPSPECIES'],filtervcf=config['references'][pfamily]['VEPFILTERVCF'],rname="pl:vcf2maf" - shell: "module load vcf2maf/1.6.12; module load samtools/1.5; module load VEP/88; vcf2maf.pl --input-vcf {input.vcf} --output-maf {output.maf} --vep-path $VEP_HOME --vep-data $VEPCACHEDIR --ref-fasta {params.genome} --filter-vcf {params.filtervcf} --vep-forks 2 --vcf-tumor-id {params.tumorsample} --vcf-normal-id {params.normalsample} --tumor-id {params.tumorsample} --normal-id {params.normalsample} --ncbi-build {params.build} --species {params.species}" + shell: "module load vcf2maf/1.6.16; module load VEP/92; vcf2maf.pl --input-vcf {input.vcf} --output-maf {output.maf} --vep-path $VEP_HOME --vep-data $VEPCACHEDIR --ref-fasta {params.genome} --filter-vcf {params.filtervcf} --vep-forks 2 --vcf-tumor-id {params.tumorsample} --vcf-normal-id {params.normalsample} --tumor-id {params.tumorsample} --normal-id {params.normalsample} --ncbi-build {params.build} --species {params.species}" rule vcf2maf_strelka: input: normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam", @@ -23,4 +23,4 @@ rule vcf2maf_strelka: output: maf=config['project']['workpath']+"/strelka_out/oncotator_out/{x}.maf", vcf=temp("strelka_out/{x}_FINAL.vep.vcf"), params: genome=config['references'][pfamily]['VEPGENOME'],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],build=config['references'][pfamily]['VEPBUILD'],species=config['references'][pfamily]['VEPSPECIES'],filtervcf=config['references'][pfamily]['VEPFILTERVCF'],rname="pl:vcf2maf" - shell: "module load vcf2maf/1.6.12; module load samtools/1.5; module load VEP/88; vcf2maf.pl --input-vcf {input.vcf} --output-maf {output.maf} --vep-path $VEP_HOME --vep-data $VEPCACHEDIR --ref-fasta {params.genome} --filter-vcf {params.filtervcf} --vep-forks 2 --vcf-tumor-id {params.tumorsample} --vcf-normal-id {params.normalsample} --tumor-id {params.tumorsample} --normal-id {params.normalsample} --ncbi-build {params.build} --species {params.species}" \ No newline at end of file + shell: "module load vcf2maf/1.6.16; module load VEP/92; vcf2maf.pl --input-vcf {input.vcf} --output-maf {output.maf} --vep-path $VEP_HOME --vep-data $VEPCACHEDIR --ref-fasta {params.genome} --filter-vcf {params.filtervcf} --vep-forks 2 --vcf-tumor-id {params.tumorsample} --vcf-normal-id {params.normalsample} --tumor-id {params.tumorsample} --normal-id {params.normalsample} --ncbi-build {params.build} --species {params.species}" \ No newline at end of file diff --git a/Rules/vcf2maf_tumoronly.rl b/Rules/vcf2maf_tumoronly.rl index 8b35724..9bcc3bd 100644 --- a/Rules/vcf2maf_tumoronly.rl +++ b/Rules/vcf2maf_tumoronly.rl @@ -3,4 +3,4 @@ rule vcf2maf_tumoronly: output: maf=config['project']['workpath']+"/mutect2_out/oncotator_out/{x}.maf", vcf=temp("mutect2_out/{x}.FINALmutect2.vep.vcf"), params: genome=config['references'][pfamily]['VEPGENOME'],tumorsample=lambda wildcards: config['project']['units'][wildcards.x],build=config['references'][pfamily]['VEPBUILD'],species=config['references'][pfamily]['VEPSPECIES'],filtervcf=config['references'][pfamily]['VEPFILTERVCF'],rname="pl:vcf2maf" - shell: "module load vcf2maf/1.6.12; module load samtools/1.5; module load VEP/88; vcf2maf.pl --input-vcf {input.vcf} --output-maf {output.maf} --vep-path $VEP_HOME --vep-data $VEPCACHEDIR --ref-fasta {params.genome} --filter-vcf {params.filtervcf} --vep-forks 2 --vcf-tumor-id {params.tumorsample} --tumor-id {params.tumorsample} --ncbi-build {params.build} --species {params.species}" \ No newline at end of file + shell: "module load vcf2maf/1.6.16; module load VEP/92; vcf2maf.pl --input-vcf {input.vcf} --output-maf {output.maf} --vep-path $VEP_HOME --vep-data $VEPCACHEDIR --ref-fasta {params.genome} --filter-vcf {params.filtervcf} --vep-forks 2 --vcf-tumor-id {params.tumorsample} --tumor-id {params.tumorsample} --ncbi-build {params.build} --species {params.species}" \ No newline at end of file diff --git a/Rules/wgs_strelka.rl b/Rules/wgs_strelka.rl index 3e9e64c..ad3ec55 100644 --- a/Rules/wgs_strelka.rl +++ b/Rules/wgs_strelka.rl @@ -9,6 +9,6 @@ rule wgs_strelka: htmlstats=config['project']['workpath']+"/strelka_out/{x}.strelka.stats.html", out=config['project']['workpath']+"/strelka_out/{x}.snpeff.out", names=temp(config['project']['workpath']+"/strelka_out/{x}.samples"), - params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],rname="pl:strelka_calls" + params: normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],dir=config['project']['workpath'],gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="pl:strelka_calls" threads: 4 - shell: "module load strelka/2.7.1; module load python; configureStrelkaSomaticWorkflow.py --ref={params.genome} --tumor={params.dir}/{input.tumor} --normal={params.dir}/{input.normal} --runDir={output.outdir}; cd {output.outdir}; ./runWorkflow.py -m local -j {threads}; {params.gatk} -T CombineVariants -R {params.genome} --variant results/variants/somatic.snvs.vcf.gz --variant results/variants/somatic.indels.vcf.gz --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL -o {output.vcf}; {params.gatk} -T SelectVariants -R {params.genome} --variant {output.vcf} --excludeFiltered -o {output.vcffiltered}; cd {params.dir}/strelka_out; module load samtools/1.5; echo $'NORMAL {params.normalsample}\nTUMOR {params.tumorsample}' > {output.names}; bcftools reheader -o {output.final} -s {output.names} {output.vcffiltered}; module load snpEff; {params.snpeff} -v {params.snpeffgenome} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.final} > {output.out}" \ No newline at end of file + shell: "module load strelka/2.9.0; module load python; configureStrelkaSomaticWorkflow.py --ref={params.genome} --tumor={params.dir}/{input.tumor} --normal={params.dir}/{input.normal} --runDir={output.outdir}; cd {output.outdir}; ./runWorkflow.py -m local -j {threads}; {params.gatk} -T CombineVariants -R {params.genome} --variant results/variants/somatic.snvs.vcf.gz --variant results/variants/somatic.indels.vcf.gz --assumeIdenticalSamples --filteredrecordsmergetype KEEP_UNCONDITIONAL -o {output.vcf}; {params.gatk} -T SelectVariants -R {params.genome} --variant {output.vcf} --excludeFiltered -o {output.vcffiltered}; cd {params.dir}/strelka_out; module load samtools/1.6; echo $'NORMAL {params.normalsample}\nTUMOR {params.tumorsample}' > {output.names}; bcftools reheader -o {output.final} -s {output.names} {output.vcffiltered}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples {params.dir}/pairs {output.final} > {output.out}" \ No newline at end of file diff --git a/hg19.json b/hg19.json index e0457fc..c6427de 100755 --- a/hg19.json +++ b/hg19.json @@ -45,7 +45,7 @@ "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC", "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA", "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz", - "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", # "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )", ###maybe change to 30 # "FILTERSIFT": "( QUAL >= 20 )", "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF", @@ -122,7 +122,7 @@ "gtfERCC": "gencode.vM4.all_ERCC.gtf", "genomeRnaseqErcc": "GRCm38.p3.ERCC.genome.fa", "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz", - "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", # "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )", ###maybe change to 30 "FILTERSIFT": "( QUAL >= 20 )", "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF", @@ -198,7 +198,7 @@ # "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC", # "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA", # "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz", - "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", "SNPEFF_GENOME": "GRCh37.75", # "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF", # "REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed", @@ -266,7 +266,7 @@ "gtfERCC": "gencode.vM4.all_ERCC.gtf", "genomeRnaseqErcc": "GRCm38.p3.ERCC.genome.fa", "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz", - "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF", "SNPEFF_GENOME": "GRCh37.75", "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed", diff --git a/hg38.json b/hg38.json index 8631a86..b76e618 100755 --- a/hg38.json +++ b/hg38.json @@ -45,7 +45,7 @@ "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC", "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA", # "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz", - "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", # "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )", ###maybe change to 30 # "FILTERSIFT": "( QUAL >= 20 )", "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF", @@ -113,7 +113,7 @@ "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC", "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA", # "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz", - "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", # "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )", ###maybe change to 30 # "FILTERSIFT": "( QUAL >= 20 )", "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF", @@ -190,7 +190,7 @@ # "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz", # "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF", "SNPEFF_GENOME": "GRCh38.82", - "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", # "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed", # "REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed", }, @@ -256,7 +256,7 @@ "gtfERCC": "gencode.vM4.all_ERCC.gtf", "genomeRnaseqErcc": "GRCm38.p3.ERCC.genome.fa", "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz", - "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF", "SNPEFF_GENOME": "GRCh37.75", "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed", diff --git a/mm10.json b/mm10.json index 4aa059d..0440f76 100755 --- a/mm10.json +++ b/mm10.json @@ -28,7 +28,7 @@ "AVIASET": "mm10", "SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz", "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/SS_mouse_exome_mm10_reformat.bed", - "SNPEFF_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", "SNPEFF_GENOME": "GRCm38.82", "FILTERSIFT": "( QUAL >= 20 )", "MUTECTGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", @@ -90,7 +90,7 @@ "AVIASET": "mm10", "SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz", "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/SS_mouse_exome_mm10_reformat.bed", - "SNPEFF_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", "SNPEFF_GENOME": "GRCm38.82", "FILTERSIFT": "( QUAL >= 20 )", "MUTECTGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", @@ -166,7 +166,7 @@ "ALVIEWGENOME": "mm10", "AVIASET": "mm10", # "SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz", - "SNPEFF_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", "SNPEFF_GENOME": "GRCm38.82", # "FILTERSIFT": "( QUAL >= 20 )", # "MUTECTGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", @@ -226,7 +226,7 @@ "ALVIEWGENOME": "mm10", "AVIASET": "mm10", "SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz", - "SNPEFF_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/snpEff.config", + "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config", "SNPEFF_GENOME": "GRCm38.82", "FILTERSIFT": "( QUAL >= 20 )", "MUTECTGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa", diff --git a/pipeline_ctrl.sh b/pipeline_ctrl.sh index 49c232b..7fc7e17 100755 --- a/pipeline_ctrl.sh +++ b/pipeline_ctrl.sh @@ -1,7 +1,7 @@ #!/bin/bash module load python/3.5 -module load perl/5.8.9 +module load perl/5.12.5 # was 5.8.9 (unsupported) #PBS -N PipelineTest diff --git a/pipeliner.py b/pipeliner.py index cb8f300..60627b8 100755 --- a/pipeliner.py +++ b/pipeliner.py @@ -675,7 +675,7 @@ def makeunitswarm(): F=open("project.json","r") config=eval(F.read()) for u in config['project']['units']: - S=S+"module load python/3.4.0; samples=\""+ u + "\"; snakemake -s Snakefile\n" + S=S+"module load python/3.5.0; samples=\""+ u + "\"; snakemake -s Snakefile\n" tkinter.messagebox.showinfo("Swarm",S) F=open("../"+PL+".swarm","w") F.write(S) @@ -686,7 +686,7 @@ def makepairswarm(): F=open("project.json","r") config=eval(F.read()) for u in config['project']['pairs'].values(): - S=S+"module load python/3.4.0; samples=\""+ ' '.join(u) + "\"; snakemake -s Snakefile\n" + S=S+"module load python/3.5.0; samples=\""+ ' '.join(u) + "\"; snakemake -s Snakefile\n" tkinter.messagebox.showinfo("Swarm",S) F=open("../"+PL+".swarm","w") F.write(S) diff --git a/rules.json b/rules.json index 47e76e9..6a59781 100755 --- a/rules.json +++ b/rules.json @@ -132,7 +132,7 @@ "database_somatic_tumoronly": ["wgs-somatic-tumoronly","exomeseq-somatic-tumoronly"], "svdetect": ["none"], "bicseq": ["none"], - "generate_QC_table": ["initialqc"], + "generate_QC_table": ["none"], "star.align": ["rnaseqvargerm"], "star.align.2": ["rnaseqvargerm"], "picard.rnaseqvar.headers": ["rnaseqvargerm"], diff --git a/slurm.template b/slurm.template index 1670d29..37a3a8d 100755 --- a/slurm.template +++ b/slurm.template @@ -9,7 +9,7 @@ D=/home/fake R=/home/fake cd $D -module load git/2.7.3 +module load git/2.15.1 git log |head -n3 > $R/Reports/ccbr_pipeliner_git_commit_version.txt cd $SLURM_SUBMIT_DIR diff --git a/standard-bin.json b/standard-bin.json old mode 100755 new mode 100644 index 95f898f..b35c5c8 --- a/standard-bin.json +++ b/standard-bin.json @@ -76,27 +76,27 @@ }, "rnaseq": { "tool_versions": { - "BOWTIE2VER" : "bowtie/2-2.3.2", - "BWAVER": "bwa/0.7.15", - "CUTADAPTVER": "cutadapt/1.14", + "BOWTIE2VER" : "bowtie/2-2.3.4", + "BWAVER": "bwa/0.7.17", + "CUTADAPTVER": "cutadapt/1.16", "FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen", "FASTQCVER" : "fastqc/0.11.5", - "KRAKENVER": "kraken/0.10.5-beta", + "KRAKENVER": "kraken/1.1", "KRONATOOLSVER": "kronatools/2.7", - "MULTIQCVER":"multiqc/1.1", - "PARALLELVER" : "parallel/20170422", - "PERLVER" : "perl/5.18.2", - "PICARDVER" : "picard/1.119", - "PIGZVER" : "pigz/2.3.4", + "MULTIQCVER":"multiqc/1.4", + "PARALLELVER" : "parallel/20171222", + "PERLVER" : "perl/5.24.3", + "PICARDVER" : "picard/2.17.11", +# "PIGZVER" : "pigz/2.3.4", "PRESEQVER": "preseq/2.0.3", "PYTHONVER" : "python/3.5", - "RMATSVER" : "mats/3.2.5", + "RMATSVER" : "rmats/4.0.1", "RSEMVER" : "rsem/1.3.0", "RSEQCVER" : "rseqc/2.6.4", - "RVER" : "R/3.4.0_gcc-6.2.0", - "SAMTOOLSVER" : "samtools/1.5", + "RVER" : "R/3.5", + "SAMTOOLSVER" : "samtools/1.6", "STARVER": "STAR/2.5.2b", - "SUBREADVER": "subread/1.5.1", + "SUBREADVER": "subread/1.5.2", "TRIMMOMATICVER": "trimmomatic/0.33", }, "tool_parameters":{ @@ -128,8 +128,8 @@ "FASTQCVER": "fastqc", "CHKQCVER": " /data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/summarizeFastQCver2", "STARVER": "STAR/2.5.2b", - "SUBREADVER": "subread/1.5.1", - "BWAVER": "bwa/0.7.10", + "SUBREADVER": "subread/1.5.2", + "BWAVER": "bwa/0.7.17", "RNASEQCJAR": "/usr/local/apps/rnaseqc/1.1.8/RNA-SeQC_v1.1.8.jar", "IOoptions": "--------------------------- Output and input locations ---------------------------------------------------------", "MYFOLDER": "/scratch/nikhil/731/", @@ -194,14 +194,14 @@ "RSEM": "/usr/local/apps/rsem/1.3.0", "FASTQC": "/usr/local/apps/fastqc/0.11.5/fastqc", "GATK": "java -Xmx64g -jar /usr/local/apps/GATK/3.5-0/GenomeAnalysisTK.jar", - "SAMTOOLS": "/usr/local/apps/samtools/1.3.1/bin/samtools", + "SAMTOOLS": "/usr/local/apps/samtools/1.6/bin/samtools", "PICARD3": "/ngs/bin/jdk1.8.0_25/bin/java -jar /ngs/bin/picard-tools-1.119/CreateSequenceDictionary.jar", "NGSQCTOOLKIT": "/usr/local/apps/ngsqctoolkit/2.3.3/QC/IlluQC.pl", - "NOVOSORT": "/usr/local/apps/novocraft/3.04.04/novosort", - "PICARD1": "module load picard/2.1.1; java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar AddOrReplaceReadGroups", - "MARKDUPS": "module load picard/2.1.1; java -Xmx16g -XX:ParallelGCThreads=12 -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar MarkDuplicates", - "QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/$SLURM_JOBID'; /usr/local/apps/qualimap/qualimap_v2.2/qualimap --java-mem-size=64G", - "SNPEFF": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/snpEff.jar", + "NOVOSORT": "/usr/local/apps/novocraft/3.08.02/novosort", + "PICARD1": "module load picard/2.17.11; java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar AddOrReplaceReadGroups", + "MARKDUPS": "module load picard/2.17.11; java -Xmx16g -XX:ParallelGCThreads=12 -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar MarkDuplicates", + "QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/$SLURM_JOBID'; /usr/local/apps/qualimap/qualimap_v2.2.1/qualimap --java-mem-size=64G", + "SNPEFF": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.3t/snpEff.jar", "TRIMMOMATIC": "java -Xmx8g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/trimmomatic/Trimmomatic-0.33/trimmomatic-0.33.jar", }, "rnaseqvargerm": { @@ -321,7 +321,7 @@ "PARALLELVER" : "parallel/20170422", "PERLVER": "perl/5.18.2", "PICARDVER": "picard/1.119", - "PIGZVER" : "pigz/2.3.4", +# "PIGZVER" : "pigz/2.3.4", "PRESEQVER": "preseq/2.0.3", "RVER": "R/3.4.0_gcc-6.2.0", "SAMTOOLSVER": "samtools/1.5", @@ -447,3 +447,4 @@ } } + diff --git a/submit_slurm.template b/submit_slurm.template index abc7918..0991eff 100755 --- a/submit_slurm.template +++ b/submit_slurm.template @@ -29,6 +29,7 @@ mv $R/Reports/makeasnake.log $R/Reports/makeasnake.log.$modtime2 touch $R/Reports/makeasnake.log touch $R/Reports/snakemake.log +#sbatch $Slrm_J --partition=centos7 --gres=lscratch:200 --time=24:00:00 --mail-type=BEGIN,END,FAIL $R/pipeline_ctrl.sh sbatch $Slrm_J --partition=ccr,norm --gres=lscratch:200 --time=120:00:00 --mail-type=BEGIN,END,FAIL $R/pipeline_ctrl.sh # sbatch --partition=ccr,norm --gres=lscratch:200 --time=120:00:00 $R/pipeline_ctrl.sh