From e066daaa51dfced6e3a523bb1827f031e4aae731 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 5 Mar 2018 12:00:36 -0600
Subject: [PATCH] java compatibility problem (snpEff uses 8) others use 7
---
variants/somatic_vc.sh | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index 2b71e0f..8530b6d 100644
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -95,10 +95,11 @@ if [ $algo == 'strelka2' ]
fi
if [ $algo == 'virmid' ]
then
- module load snpeff/4.3q virmid/1.2 samtools/1.6 vcftools/0.1.14
+ module load virmid/1.2 samtools/1.6 vcftools/0.1.14
virmid -R ${reffa} -D ${tumor} -N ${normal} -s ${cosmic} -t $SLURM_CPUS_ON_NODE -M 2000 -c1 10 -c2 10
perl $baseDir/addgt_virmid.pl ${tumor}.virmid.som.passed.vcf
perl $baseDir/addgt_virmid.pl ${tumor}.virmid.loh.passed.vcf
+ module load snpeff/4.3q
vcf-concat *gt.vcf | vcf-sort | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter '((NDP >= 10) & (DDP >= 10))' | perl -pe "s/TUMOR/${tid}/g" | perl -pe "s/NORMAL/${nid}/g" | bgzip > ${pair_id}.virmid.vcf.gz
fi
@@ -123,12 +124,13 @@ fi
if [ $algo == 'varscan' ]
then
- module load snpeff/4.3q samtools/1.6 VarScan/2.4.2 speedseq/20160506 vcftools/0.1.14
+ module load samtools/1.6 VarScan/2.4.2 speedseq/20160506 vcftools/0.1.14
sambamba mpileup --tmpdir=./ -t $SLURM_CPUS_ON_NODE ${tumor} --samtools "-C 50 -f ${reffa}" > t.mpileup
sambamba mpileup --tmpdir=./ -t $SLURM_CPUS_ON_NODE ${normal} --samtools "-C 50 -f ${reffa}" > n.mpileup
VarScan somatic n.mpileup t.mpileup vscan --output-vcf 1
- VarScan copynumber n.mpileup t.mpileup vscancnv
- 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 > ${tid}_${nid}.varscan.vcf.gz
+ VarScan copynumber n.mpileup t.mpileup vscancnv
+ module load snpeff/4.3q
+ 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
fi
if [ $algo == 'shimmer' ]
--
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