Merge pull request #404 from jlac/activeDev

improved somatic variant filtering and maftools summaries
CCBR · Feb 21, 2019 · df316c9 · df316c9
2 parents 1039f14 + 8a9a669
commit df316c9
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/Results-template/Scripts/maftools.R b/Results-template/Scripts/maftools.R
@@ -22,5 +22,5 @@ pdf(FILE2)
 plotmafSummary(mymaf)
 dev.off()
 pdf(FILE3)
-oncoplot(mymaf,writeMatrix=TRUE,showTumorSampleBarcodes=TRUE,genesToIgnore=flags)
+oncoplot(mymaf,writeMatrix=TRUE,showTumorSampleBarcodes=TRUE,genesToIgnore=flags,removeNonMutated=FALSE)
 dev.off()
diff --git a/Results-template/Scripts/prep_mafs.pl b/Results-template/Scripts/prep_mafs.pl
@@ -42,7 +42,7 @@
 		next if ($line[0] =~ /TTN|MUC16|OBSCN|AHNAK2|SYNE1|FLG|MUC5B|DNAH17|PLEC|DST|SYNE2|NEB|HSPG2|LAMA5|AHNAK|HMCN1|USH2A|DNAH11|MACF1|MUC17|DNAH5|GPR98|FAT1|PKD1|MDN1|RNF213|RYR1|DNAH2|DNAH3|DNAH8|DNAH1|DNAH9|ABCA13|SRRM2|CUBN|SPTBN5|PKHD1|LRP2|FBN3|CDH23|DNAH10|FAT4|RYR3|PKHD1L1|FAT2|CSMD1|PCNT|COL6A3|FRAS1|FCGBP|RYR2|HYDIN|XIRP2|LAMA1/);
 		if (($line[44] eq '-') || ($line[44] < 2)) {
 			if (($line[41] > 2) && ($line[39] > 9)) {
-				if ((($line[123] eq '-') || ($line[123] < 0.001)) && (($line[76] eq '-') || ($line[76] < 0.01)) && (($line[99] eq '-') || ($line[99] < 0.001))) {
+				if ((($line[123] eq '-') || ($line[123] < 0.001)) && (($line[76] eq '-') || ($line[76] < 0.01)) && (($line[99] eq '-') || ($line[99] < 0.001)) && (($line[41]/$line[39]) > 0.05) {
 					print C "$_\t";
 					if ($line[39] != 0){
 						$calc=($line[41]/$line[39]);

diff --git 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/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ mutect2_variants.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.mutect2oncoprint}; Rscript Scripts/maftools.R {params.dir}/mutect_out/oncotator_out/ mutect_variants.maf {params.dir}/mutect_out/mutect_maf_summary.pdf {output.mutectoncoprint}; Rscript Scripts/maftools.R {params.dir}/strelka_out/oncotator_out/ strelka_variants.maf {params.dir}/strelka_out/strelka_maf_summary.pdf {output.strelkaoncoprint}"
+  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/ final_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.mutect2oncoprint}; Rscript Scripts/maftools.R {params.dir}/mutect_out/oncotator_out/ final_filtered.maf {params.dir}/mutect_out/mutect_maf_summary.pdf {output.mutectoncoprint}; Rscript Scripts/maftools.R {params.dir}/strelka_out/oncotator_out/ final_filtered.maf {params.dir}/strelka_out/strelka_maf_summary.pdf {output.strelkaoncoprint}"