From 2079d56d2a35e4fac461481c2afc7991054621db Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 29 Jul 2020 11:17:27 -0500
Subject: [PATCH] update mutect to take intervals remove parallel
---
variants/germline_vc.sh | 2 +-
variants/somatic_vc.sh | 6 +++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 1bc6a07..3ce4680 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -136,7 +136,7 @@ then
for i in *.bam; do
bamlist+="-I ${i} "
done
- cut -f 1 intervals.txt | parallel --delay 1 --jobs $threads "gatk --java-options \"-Xmx20g\" Mutect2 $ponopt -R ${reffa} ${bamlist} -RF AllowAllReadsReadFilter --independent-mates --tmp-dir `pwd` --output ${pair_id}.mutect.{}.vcf -L {}"
+ gatk --java-options "-Xmx20g" Mutect2 $ponopt -R ${reffa} ${bamlist} --output ${pair_id}.mutect.vcf -RF AllowAllReadsReadFilter --independent-mates --tmp-dir `pwd` -L $interval
vcf-sort ${pair_id}.mutect.vcf | vcf-annotate -n --fill-type | java -jar $SNPEFF_HOME/SnpSift.jar filter -p '(GEN[*].DP >= 10)' | bgzip > ${pair_id}.mutect.vcf.gz
elif [[ $algo == 'strelka2' ]]
then
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index be5a185..dcfce30 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -82,10 +82,10 @@ else
fi
baseDir="`dirname \"$0\"`"
-cat ${reffa}.fai |cut -f 1 |grep -v decoy |grep -v 'HLA' |grep -v alt |grep -v 'chrUn' |grep -v 'random' > intervals.txt
+interval=`cat ${reffa}.fai |cut -f 1 |grep -v decoy |grep -v 'HLA' |grep -v alt |grep -v 'chrUn' |grep -v 'random' | perl -pe 's/\n/ -L /g' |perl -pe 's/-L $//'`
if [[ -n $tbed ]]
then
- awk '{print $1":"$2"-"$3}' $tbed > intervals.txt
+ interval=$tbed
fi
if [[ -z $tid ]]
then
@@ -138,7 +138,7 @@ then
gatk4_dbsnp=${index_path}/clinseq_prj/dbSnp.gatk4.vcf.gz
module load gatk/4.1.4.0 parallel/20150122
threads=`expr $NPROC / 2`
- cut -f 1 intervals.txt | parallel --delay 1 --jobs $threads "gatk --java-options \"-Xmx20g\" Mutect2 $ponopt --independent-mates -RF AllowAllReadsReadFilter -R ${reffa} -I ${tumor} -tumor ${tid} -I ${normal} -normal ${nid} --output ${tid}.mutect.{}.vcf -L {}"
+ gatk --java-options "-Xmx20g" Mutect2 $ponopt --independent-mates -RF AllowAllReadsReadFilter -R ${reffa} -I ${tumor} -tumor ${tid} -I ${normal} -normal ${nid} --output ${tid}.mutect.vcf -L $interval
vcf-concat ${tid}.mutect.*vcf | vcf-sort | vcf-annotate -n --fill-type | java -jar $SNPEFF_HOME/SnpSift.jar filter -p '(GEN[*].DP >= 10)' | bgzip > ${pair_id}.mutect.vcf.gz
elif [ $algo == 'varscan' ]
then
--
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