From a0bd27af7da973a161da415b893f5a5fc3b1ba88 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 19 Sep 2018 19:12:46 -0500
Subject: [PATCH] mutect to gatk3.8
---
variants/somatic_callers.sh | 2 +-
variants/somatic_vc.sh | 12 ++++++------
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/variants/somatic_callers.sh b/variants/somatic_callers.sh
index 9b9da36..4517c52 100755
--- a/variants/somatic_callers.sh
+++ b/variants/somatic_callers.sh
@@ -75,7 +75,7 @@ fi
if [ $algo == 'mutect' ]
then
- module load parallel python/2.7.x-anaconda gatk/3.5 bcftools/intel/1.3 bedtools/2.25.0 snpeff/4.2 vcftools/0.1.14
+ module load parallel python/2.7.x-anaconda gatk/3.8 bcftools/intel/1.3 bedtools/2.25.0 snpeff/4.2 vcftools/0.1.14
cut -f 1 /project/shared/bicf_workflow_ref/GRCh38/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Xmx20g -jar $GATK_JAR -R ${genome_reference} -D ${dbSnp_reference} -T MuTect2 -stand_call_conf 30 -stand_emit_conf 10.0 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -I:tumor ${tumor}.final.bam -I:normal ${normal}.final.bam --cosmic ${cosmic} -o ${tumor}.{}.mutect.vcf -L {}"
vcf-concat ${tumor}*.vcf | vcf-sort | vcf-annotate -n --fill-type | java -jar $SNPEFF_HOME/SnpSift.jar filter -p '((FS <= 60) & GEN[*].DP >= 10)' | perl -pe 's/TUMOR/'${tumor}'/' | perl -pe 's/NORMAL/'${normal}'/g' |bgzip > ${tumor}_${normal}.mutect.vcf.gz
fi
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index 3e43d77..207ac1b 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -113,7 +113,7 @@ fi
if [ $algo == 'mutect2' ]
then
- module load parallel gatk/3.7 snpeff/4.3q samtools/1.6 vcftools/0.1.14
+ module load parallel gatk/3.8 snpeff/4.3q samtools/1.6 vcftools/0.1.14
if [ -z ${tbed} ]
then
cut -f 1 ${index_path}/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Xmx20g -jar \$GATK_JAR -R ${reffa} -D ${dbsnp} -T MuTect2 -stand_call_conf 10 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -I:tumor ${tumor} -I:normal ${normal} --cosmic ${cosmic} -o ${tid}.{}.mutect.vcf -L {}"
@@ -125,13 +125,13 @@ fi
if [ $algo == 'varscan' ]
then
- 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
+ module load samtools/1.6 VarScan/2.4.2 vcftools/0.1.14
module rm java/oracle/jdk1.7.0_51
module load snpeff/4.3q
+ samtools mpileup -C 50 -f ${reffa} $tumor > t.mpileup
+ samtools mpileup -C 50 -f ${reffa} $normal > t.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 > ${pair_id}.varscan.vcf.gz
fi
--
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