From 23e205b9e92a7425ad44109dc9573a056e1a68bd Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 8 Dec 2017 16:41:20 -0600
Subject: [PATCH] lancet update
---
variants/somatic_vc.sh | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index 37bc444..23b53ac 100644
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -80,7 +80,7 @@ baseDir="`dirname \"$0\"`"
if [ $algo == 'strelka2' ]
then
- module load strelka/2.8.3 manta/1.2.0 snpeff/4.3q vcftools/0.1.14
+ module load strelka/2.8.3 samtools/1.6 manta/1.2.0 snpeff/4.3q vcftools/0.1.14
mkdir manta strelka
configManta.py --normalBam ${normal} --tumorBam ${tumor} --referenceFasta ${reffa} --runDir manta
manta/runWorkflow.py -m local -j 8
@@ -91,7 +91,7 @@ fi
if [ $algo == 'virmid' ]
then
- module load snpeff/4.3q virmid/1.2 vcftools/0.1.14
+ module load snpeff/4.3q 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
@@ -100,14 +100,14 @@ fi
if [ $algo == 'speedseq' ]
then
- module load snpeff/4.3q speedseq/20160506 vcftools/0.1.14
+ module load snpeff/4.3q speedseq/20160506 samtools/1.6 vcftools/0.1.14
speedseq somatic -q 10 -t $SLURM_CPUS_ON_NODE -o sssom ${reffa} ${normal} ${tumor}
vcf-annotate -H -n --fill-type sssom.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter '((QUAL >= 10) & (GEN[*].DP >= 10))' | perl -pe 's/TUMOR/${tid}/' | perl -pe 's/NORMAL/${nid}/g' |bgzip > ${pair_id}.sssom.vcf.gz
fi
if [ $algo == 'mutect2' ]
then
- module load parallel gatk/3.7 snpeff/4.3q vcftools/0.1.14
+ module load parallel gatk/3.7 snpeff/4.3q samtools/1.6 vcftools/0.1.14
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 {}"
vcf-concat ${tid}*.vcf | vcf-sort | vcf-annotate -n --fill-type | java -jar \$SNPEFF_HOME/SnpSift.jar filter -p '((FS <= 60) & GEN[*].DP >= 10)' | perl -pe 's/TUMOR/${tid}/' | perl -pe 's/NORMAL/${nid}/g' |bgzip > ${pair_id}.pmutect.vcf.gz
fi
@@ -115,8 +115,8 @@ fi
if [ $algo == 'varscan' ]
then
module load snpeff/4.3q samtools/1.6 VarScan/2.4.2 speedseq/20160506 vcftools/0.1.14
- sambamba mpileup -t $SLURM_CPUS_ON_NODE ${tumor} --samtools "-C 50 -f ${reffa}" > t.mpileup
- sambamba mpileup -t $SLURM_CPUS_ON_NODE ${normal} --samtools "-C 50 -f ${reffa}" > n.mpileup
+ 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
@@ -124,7 +124,7 @@ fi
if [ $algo == 'shimmer' ]
then
- module load snpeff/4.3q shimmer/0.1.1 vcftools/0.1.14
+ module load snpeff/4.3q shimmer/0.1.1 samtools/1.6 vcftools/0.1.14
shimmer.pl --minqual 25 --ref ${reffa} ${normal} ${tumor} --outdir shimmer 2> shimmer.err
perl /project/PHG/PHG_Clinical/clinseq_workflows/scripts/add_readct_shimmer.pl
vcf-annotate -n --fill-type shimmer/somatic_diffs.readct.vcf | java -jar $SNPEFF_HOME/SnpSift.jar filter '(GEN[*].DP >= 10)' | perl -pe 's/TUMOR/${tid}/' | perl -pe 's/NORMAL/${nid}/g' | bgzip > ${pair_id}.shimmer.vcf.gz
@@ -132,7 +132,7 @@ fi
if [ $algo == 'lancet' ]
then
- module load snpeff/4.3q lancet vcftools/0.1.14
- lancet --tumor ${tumor} --normal ${normal} --ref $reffa -B $tbed --num-threads 16 > lancet.vcf
- vcf-sort lancet.vcf | vcf-annotate -n --fill-type -n | perl -pe 's/TUMOR/${tid}/' | perl -pe 's/NORMAL/${nid}/g' |bgzip > ${pair_id}.lancet.vcf.gz
+ module load snpeff/4.3q lancet samtools/1.6 vcftools/0.1.14
+ lancet --tumor ${tumor} --normal ${normal} --ref $reffa -B $tbed --num-threads $SLURM_CPUS_ON_NODE > lancet.vcf
+ vcf-sort lancet.vcf | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter "((FILTER = 'PASS') | (FILTER = 'LowVafTumor') | (FILTER = 'LowVafTumor;LowAltCntTumor')) & (GEN[*].DP >= 10)" |bgzip > ${pair_id}.lancet.vcf.gz
fi
--
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