switch VarDict to java version for faster run time

Results-template/Scripts/maftools.R

@@ -10,8 +10,8 @@ mymaf <- read.maf(FILE1)
 flags <- c("TTN","MUC16","OBSCN","AHNAK2","SYNE1","FLG","MUC5B","DNAH17","PLEC","DST","SYNE2","NEB","HSPG2","LAMA5","AHNAK","HMCN1","USH2A","DNAH11","MACF1","MUC17","DNAH5","GPR98","FAT1","PKD1","MDN1","RNF213","RYR1","DNAH2","DNAH3","DNAH8","DNAH1","DNAH9","ABCA13","SRRM2","CUBN","SPTBN5","PKHD1","LRP2","FBN3","CDH23","DNAH10","FAT4","RYR3","PKHD1L1","FAT2","CSMD1","PCNT","COL6A3","FRAS1","FCGBP","RYR2","HYDIN","XIRP2","LAMA1")
 samplesum<-getSampleSummary(mymaf)
 genesum<-getGeneSummary(mymaf)
-write.table(samplesum,file="sample_summary.txt",sep="\t")
-write.table(genesum,file="gene_summary.txt",sep="\t")
+write.table(samplesum,file="sample_summary.txt",sep="\t",quote = FALSE,row.names = FALSE)
+write.table(genesum,file="gene_summary.txt",sep="\t",quote = FALSE,row.names = FALSE)
 pdf('tcga_comparison.pdf')
 tcgaCompare(maf=mymaf,cohortName = "project_variants")
 dev.off()

Rules/maftools.rl

@@ -5,7 +5,7 @@ rule maftools_mutect2:
           summary=config['project']['workpath']+"/mutect2_out/mutect2_maf_summary.pdf",
           oncoprint=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_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ final_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > mutect2_out/oncotator_out/mutect2_variants.maf; perl Scripts/prep_mafs.pl mutect2_out/oncotator_out/mutect2_variants.maf mutect2_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ final_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.oncoprint}"
 
 rule maftools_mutect:
   input: expand(config['project']['workpath']+"/mutect_out/oncotator_out/{x}.maf",x=pairs),
@@ -14,7 +14,7 @@ rule maftools_mutect:
           summary=config['project']['workpath']+"/mutect_out/mutect_maf_summary.pdf",
           oncoprint=config['project']['workpath']+"/mutect_out/mutect_oncoplot.pdf",
   params: dir=config['project']['workpath'],rname="pl:maftools"
-  shell: "cat mutect_out/oncotator_out/*.maf > mutect_out/oncotator_out/mutect_variants.maf; perl Scripts/prep_mafs.pl mutect_out/oncotator_out/mutect_variants.maf mutect_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect_out/oncotator_out/ final_filtered.maf {params.dir}/mutect_out/mutect_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > mutect_out/oncotator_out/mutect_variants.maf; perl Scripts/prep_mafs.pl mutect_out/oncotator_out/mutect_variants.maf mutect_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect_out/oncotator_out/ final_filtered.maf {params.dir}/mutect_out/mutect_maf_summary.pdf {output.oncoprint}"
 
 rule maftools_strelka:
   input: expand(config['project']['workpath']+"/strelka_out/oncotator_out/{x}.maf",x=pairs),
@@ -23,7 +23,7 @@ rule maftools_strelka:
           summary=config['project']['workpath']+"/strelka_out/strelka_maf_summary.pdf",
           oncoprint=config['project']['workpath']+"/strelka_out/strelka_oncoplot.pdf",
   params: dir=config['project']['workpath'],rname="pl:maftools"
-  shell: "cat strelka_out/oncotator_out/*.maf > strelka_out/oncotator_out/strelka_variants.maf; perl Scripts/prep_mafs.pl strelka_out/oncotator_out/strelka_variants.maf strelka_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/strelka_out/oncotator_out/ final_filtered.maf {params.dir}/strelka_out/strelka_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > strelka_out/oncotator_out/strelka_variants.maf; perl Scripts/prep_mafs.pl strelka_out/oncotator_out/strelka_variants.maf strelka_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/strelka_out/oncotator_out/ final_filtered.maf {params.dir}/strelka_out/strelka_maf_summary.pdf {output.oncoprint}"
 
 rule maftools_vardict:
   input: expand(config['project']['workpath']+"/vardict_out/oncotator_out/{x}.maf",x=pairs),
@@ -32,7 +32,7 @@ rule maftools_vardict:
           summary=config['project']['workpath']+"/vardict_out/vardict_maf_summary.pdf",
           oncoprint=config['project']['workpath']+"/vardict_out/vardict_oncoplot.pdf",
   params: dir=config['project']['workpath'],rname="pl:maftools"
-  shell: "cat vardict_out/oncotator_out/*.maf > vardict_out/oncotator_out/vardict_variants.maf; perl Scripts/prep_mafs.pl vardict_out/oncotator_out/vardict_variants.maf vardict_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/vardict_out/oncotator_out/ final_filtered.maf {params.dir}/vardict_out/vardict_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > vardict_out/oncotator_out/vardict_variants.maf; perl Scripts/prep_mafs.pl vardict_out/oncotator_out/vardict_variants.maf vardict_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/vardict_out/oncotator_out/ final_filtered.maf {params.dir}/vardict_out/vardict_maf_summary.pdf {output.oncoprint}"
 
 rule maftools_merged:
   input: expand(config['project']['workpath']+"/merged_somatic_variants/oncotator_out/{x}.maf",x=pairs),
@@ -41,4 +41,4 @@ rule maftools_merged:
           summary=config['project']['workpath']+"/merged_somatic_variants/merged_maf_summary.pdf",
           oncoprint=config['project']['workpath']+"/merged_somatic_variants/merged_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/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ final_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > merged_somatic_variants/oncotator_out/merged_variants.maf; perl Scripts/prep_mafs.pl merged_somatic_variants/oncotator_out/merged_variants.maf merged_somatic_variants; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/merged_somatic_variants/oncotator_out/ final_filtered.maf {params.dir}/merged_somatic_variants/merged_maf_summary.pdf {output.oncoprint}"

Rules/maftools_tumoronly.rl

@@ -5,7 +5,7 @@ rule maftools_mutect2_tumoronly:
           summary=config['project']['workpath']+"/mutect2_out/mutect2_maf_summary.pdf",
           oncoprint=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_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ final_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > mutect2_out/oncotator_out/mutect2_variants.maf; perl Scripts/prep_mafs.pl mutect2_out/oncotator_out/mutect2_variants.maf mutect2_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ final_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.oncoprint}"
 
 rule maftools_tumoronly_mutect:
   input: mutectmaf=expand(config['project']['workpath']+"/mutect_out/oncotator_out/{s}.maf",s=samples),
@@ -14,7 +14,7 @@ rule maftools_tumoronly_mutect:
           summary=config['project']['workpath']+"/mutect_out/mutect_maf_summary.pdf",
           oncoprint=config['project']['workpath']+"/mutect_out/mutect_oncoplot.pdf",
   params: dir=config['project']['workpath'],rname="pl:maftools"
-  shell: "cat mutect_out/oncotator_out/*.maf > mutect_out/oncotator_out/mutect_variants.maf; perl Scripts/prep_mafs.pl mutect_out/oncotator_out/mutect_variants.maf mutect_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect_out/oncotator_out/ final_filtered.maf {params.dir}/mutect_out/mutect_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > mutect_out/oncotator_out/mutect_variants.maf; perl Scripts/prep_mafs.pl mutect_out/oncotator_out/mutect_variants.maf mutect_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect_out/oncotator_out/ final_filtered.maf {params.dir}/mutect_out/mutect_maf_summary.pdf {output.oncoprint}"
 
 rule maftools_tumoronly_vardict:
   input: vardictmaf=expand(config['project']['workpath']+"/vardict_out/oncotator_out/{s}.maf",s=samples),
@@ -23,7 +23,7 @@ rule maftools_tumoronly_vardict:
           summary=config['project']['workpath']+"/vardict_out/vardict_maf_summary.pdf",
           oncoprint=config['project']['workpath']+"/vardict_out/vardict_oncoplot.pdf",
   params: dir=config['project']['workpath'],rname="pl:maftools"
-  shell: "cat vardict_out/oncotator_out/*.maf > vardict_out/oncotator_out/vardict_variants.maf; perl Scripts/prep_mafs.pl vardict_out/oncotator_out/vardict_variants.maf vardict_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/vardict_out/oncotator_out/ final_filtered.maf {params.dir}/vardict_out/vardict_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > vardict_out/oncotator_out/vardict_variants.maf; perl Scripts/prep_mafs.pl vardict_out/oncotator_out/vardict_variants.maf vardict_out; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/vardict_out/oncotator_out/ final_filtered.maf {params.dir}/vardict_out/vardict_maf_summary.pdf {output.oncoprint}"
 
 rule maftools_tumoronly_merged:
   input: mergedmaf=expand(config['project']['workpath']+"/merged_somatic_variants/oncotator_out/{s}.maf",s=samples),
@@ -32,4 +32,4 @@ rule maftools_tumoronly_merged:
           summary=config['project']['workpath']+"/merged_somatic_variants/merged_maf_summary.pdf",
           oncoprint=config['project']['workpath']+"/merged_somatic_variants/merged_oncoplot.pdf",
   params: dir=config['project']['workpath'],rname="pl:maftools"
-  shell: "cat merged_somatic_variants/oncotator_out/*.maf > merged_somatic_variants/oncotator_out/merged_variants.maf; perl Scripts/prep_mafs.pl merged_somatic_variants/oncotator_out/merged_variants.maf merged_somatic_variants; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/merged_somatic_variants/oncotator_out/ final_filtered.maf {params.dir}/merged_somatic_variants/merged_maf_summary.pdf {output.oncoprint}"
+  shell: "cat {input} > merged_somatic_variants/oncotator_out/merged_variants.maf; perl Scripts/prep_mafs.pl merged_somatic_variants/oncotator_out/merged_variants.maf merged_somatic_variants; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/merged_somatic_variants/oncotator_out/ final_filtered.maf {params.dir}/merged_somatic_variants/merged_maf_summary.pdf {output.oncoprint}"

Rules/merge_somatic_vcfs.rl

@@ -8,4 +8,4 @@ rule merge_somatic_vcfs:
             htmlstats=config['project']['workpath']+"/merged_somatic_variants/{x}.mutect.stats.html",
             out=config['project']['workpath']+"/merged_somatic_variants/{x}.snpeff.out",
     params: gres="lscratch:100",gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],snpeffgenome=config['references'][pfamily]['SNPEFF_GENOME'],snpeff=config['bin'][pfamily]['SNPEFF'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],rname="CombineVariants"
-    shell: "mkdir -p merged_somatic_variants; module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T CombineVariants -R {params.genome} -nt 8 --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED --genotypemergeoption PRIORITIZE --rod_priority_list mutect2,mutect,strelka,vardict -o {output.mergedvcf} --variant:mutect {input.mutect} --variant:strelka {input.strelka} --variant:mutect2 {input.mutect2} --variant:vardict {input.vardict}; module load snpEff/4.3t; java -Xmx12g -jar $SNPEFF_JAR -v {params.snpeffgenome} -c {params.effconfig} -cancer -canon -csvStats {output.csvstats} -stats {output.htmlstats} -cancerSamples pairs {output.mergedvcf} > {output.out}"
+    shell: "mkdir -p merged_somatic_variants; module load GATK/3.8-0; java -Xmx48g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $GATK_JAR -T CombineVariants -R {params.genome} -nt 8 --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED --genotypemergeoption PRIORITIZE --rod_priority_list mutect2,mutect,strelka,vardict --minimumN 2 -o {output.mergedvcf} --variant:mutect {input.mutect} --variant:strelka {input.strelka} --variant:mutect2 {input.mutect2} --variant:vardict {input.vardict}; 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 pairs {output.mergedvcf} > {output.out}"

Rules/vardict.rl

@@ -4,10 +4,10 @@ rule vardict:
                targets=config['project']['workpath']+"/exome_targets.bed",
                normalbai=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
                tumorbai=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
-       output: vcf=temp(config['project']['workpath']+"/vardict_out/{x}.vcf"),
+       output: vcf=config['project']['workpath']+"/vardict_out/{x}.vcf",
                filtvcf=config['project']['workpath']+"/vardict_out/{x}.FINAL.vcf",
                csvstats=config['project']['workpath']+"/vardict_out/{x}.vardict.stats.csv",
                htmlstats=config['project']['workpath']+"/vardict_out/{x}.vardict.stats.html",
                out=config['project']['workpath']+"/vardict_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'],effconfig=config['references'][pfamily]['SNPEFF_CONFIG'],pon=config['references'][pfamily]['PON'],rname="pl:vardict"
-       shell:  "mkdir -p vardict_out; module load R/3.5; module load samtools/1.9; /data/CCBR_Pipeliner/db/PipeDB/bin/VarDict/vardict -G {params.genome} -f 0.05 -x 1000 -N {params.tumorsample} --nosv -b \"{input.tumor}|{input.normal}\" -t -Q 20 -c 1 -S 2 -E 3 {params.targets} | /data/CCBR_Pipeliner/db/PipeDB/bin/VarDict/testsomatic.R | /data/CCBR_Pipeliner/db/PipeDB/bin/VarDict/var2vcf_paired.pl -N {params.tumorsample} -f 0.05 > {output.vcf}; module load GATK/3.8-0; module load java/1.8.0_92; GATK -m 48G SelectVariants -R {params.genome} --variant {output.vcf} --excludeFiltered --discordance {params.pon} -o {output.filtvcf}; 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.filtvcf} > {output.out}"
+       shell:  "mkdir -p vardict_out; module load R/3.5; module load samtools/1.9; /data/CCBR_Pipeliner/db/PipeDB/bin/VarDictJava/build/install/VarDict/bin/VarDict -G {params.genome} -f 0.05 -x 500 -N \"{params.tumorsample}|{params.normalsample}\" --nosv -b \"{input.tumor}|{input.normal}\" -t -Q 20 -c 1 -S 2 -E 3 {params.targets} | /data/CCBR_Pipeliner/db/PipeDB/bin/VarDictJava/build/install/VarDict/bin/testsomatic.R | /data/CCBR_Pipeliner/db/PipeDB/bin/VarDictJava/build/install/VarDict/bin/var2vcf_paired.pl -S -Q 20 -d 10 -M -N \"{params.tumorsample}|{params.normalsample}\" -f 0.05 > {output.vcf}; module load GATK/3.8-0; module load java/1.8.0_92; GATK -m 48G SelectVariants -R {params.genome} --variant {output.vcf} --excludeFiltered --discordance {params.pon} -o {output.filtvcf}; 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.filtvcf} > {output.out}"

Rules/vardict_tumoronly.rl

@@ -8,4 +8,4 @@ rule vardict_tumoronly:
                csvstats=config['project']['workpath']+"/vardict_out/{x}.vardict.stats.csv",
                htmlstats=config['project']['workpath']+"/vardict_out/{x}.vardict.stats.html",
        params: sample="{x}",pon=config['references'][pfamily]['PON'],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:vardict"
-       shell:  "mkdir -p vardict_out; module load R/3.5; module load samtools/1.9; /data/CCBR_Pipeliner/db/PipeDB/bin/VarDict/vardict -G {params.genome} -f 0.05 -x 1000 --nosv -b {input.tumor} -t -Q 20 -c 1 -S 2 -E 3 {params.targets} | /data/CCBR_Pipeliner/db/PipeDB/bin/VarDict/teststrandbias.R | /data/CCBR_Pipeliner/db/PipeDB/bin/VarDict/var2vcf_valid.pl -N {params.sample} -S -E -f 0.05 > {output.vcf}; module load GATK/3.8-0; module load java/1.8.0_92; GATK -m 48G SelectVariants -R {params.genome} --variant {output.vcf} --discordance {params.pon} -o {output.filtvcf}; 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 pairs {output.filtvcf} > {output.out}"
+       shell:  "mkdir -p vardict_out; module load R/3.5; module load samtools/1.9; /data/CCBR_Pipeliner/db/PipeDB/bin/VarDictJava/build/install/VarDict/bin/VarDict -G {params.genome} -f 0.05 -x 500 --nosv -b {input.tumor} -t -Q 20 -c 1 -S 2 -E 3 {params.targets} | /data/CCBR_Pipeliner/db/PipeDB/bin/VarDictJava/build/install/VarDict/bin/teststrandbias.R | /data/CCBR_Pipeliner/db/PipeDB/bin/VarDictJava/build/install/VarDict/bin/var2vcf_valid.pl -N {params.sample} -Q 20 -d 10 -v 6 -S -E -f 0.05 > {output.vcf}; module load GATK/3.8-0; module load java/1.8.0_92; GATK -m 48G SelectVariants -R {params.genome} --variant {output.vcf} --discordance {params.pon} -o {output.filtvcf}; 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 pairs {output.filtvcf} > {output.out}"