From ce95821bda995b03b5ed6ae14dbf7d0045d20b84 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 19 Jun 2020 15:58:30 -0500
Subject: [PATCH] update shimmer; update filter to not remove MSI2 gene
---
variants/filter_cnvkit.pl | 4 ++--
variants/somatic_vc.sh | 3 ++-
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index 772feaf..ef06a3e 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -54,7 +54,7 @@ while (my $line = <CNR>) {
} else {
my @ids = split(/,/,$geneids);
foreach my $gid (@ids) {
- next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI/);
+ next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI:/);
my ($gene,@other) = split(/:/,$gid);
my ($gname,@loc) = split(/_/,$gene);
$genes{$gname} = 1;
@@ -93,7 +93,7 @@ while (my $line = <IN>) {
} else {
my @ids = split(/,/,$geneids);
foreach my $gid (@ids) {
- next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI/);
+ next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion|MSI:/);
my ($gene,@other) = split(/:/,$gid);
my ($gname,@loc) = split(/_/,$gene);
$genes{$gname} = 1;
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index b6ec609..4631780 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -90,6 +90,7 @@ baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh
module load htslib/gcc/1.8
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
if [ $algo == 'strelka2' ]
then
@@ -140,7 +141,7 @@ then
vcf-concat vscan*.vcf | vcf-sort | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter '((exists SOMATIC) & (GEN[*].DP >= 10))' | perl -pe "s/TUMOR/${tid}/" | perl -pe "s/NORMAL/${nid}/g" | bgzip > ${pair_id}.varscan.vcf.gz
elif [ $algo == 'shimmer' ]
then
- module load shimmer/0.1.1 samtools/gcc/1.8 vcftools/0.1.14
+ module load samtools/gcc/1.8 R/3.6.1-gccmkl vcftools/0.1.14
shimmer.pl --minqual 25 --ref ${reffa} ${normal} ${tumor} --outdir shimmer 2> shimmer.err
perl $baseDir/add_readct_shimmer.pl
module rm java/oracle/jdk1.7.0_51
--
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