From 87e71f14028fe5863463351d7c64977548fdf473 Mon Sep 17 00:00:00 2001
From: Erika Villa <Erika.Villa@utsouthwestern.edu>
Date: Tue, 28 Nov 2017 09:55:24 -0600
Subject: [PATCH] fix varscan option
---
variants/somatic_callers.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/variants/somatic_callers.sh b/variants/somatic_callers.sh
index 99c6870..8163313 100644
--- a/variants/somatic_callers.sh
+++ b/variants/somatic_callers.sh
@@ -83,7 +83,7 @@ if [ $algo == 'varscan' ]
then
module load python/2.7.x-anaconda bedtools/2.25.0 snpeff/4.2 bcftools/intel/1.3 samtools/intel/1.3 VarScan/2.4.2 speedseq/20160506 vcftools/0.1.14
sambamba mpileup -L ${target_bed} -t $SLURM_CPUS_ON_NODE ${tumor}.final.bam --samtools "-C 50 -f ${genome_reference}" > t.mpileup
- sambamba mpileup -L ${target_bed} -t $SLURM_CPUS_ON_NODE ${normal} --samtools "-C 50 -f ${genome_reference}" > n.mpileup
+ sambamba mpileup -L ${target_bed} -t $SLURM_CPUS_ON_NODE ${normal}.final.bam --samtools "-C 50 -f ${genome_reference}" > n.mpileup
VarScan somatic n.mpileup t.mpileup ${tumor}.vscan --output-vcf 1
VarScan copynumber n.mpileup t.mpileup ${tumor}.vscancnv
vcf-concat ${tumor}.vscan*.vcf | vcf-sort | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter '((exists SOMATIC) & (GEN[*].DP >= 10))' | perl -pe 's/TUMOR/'${tumor}'/' | perl -pe 's/NORMAL/'${normal}'/g' |bedtools intersect -header -a stdin -b ${target_bed} |bgzip > ${tumor}_${normal}.varscan.vcf.gz
--
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