From 1c4a837ac18d68a3a01c4cf4a951f2d196f73bf8 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 29 Jul 2020 14:46:23 -0500
Subject: [PATCH] update strelka file
---
variants/germline_vc.sh | 12 ++++++++++--
variants/somatic_vc.sh | 10 +++++-----
2 files changed, 15 insertions(+), 7 deletions(-)
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 3ce4680..cd1a1c7 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -100,7 +100,7 @@ then
for i in *.bam; do
bamlist="$bamlist --bam ${PWD}/${i}"
done
- cut -f 1 $fbsplit | parallel --delay 1 --jobs 0 "freebayes -f ${index_path}/genome.fa --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
+ cut -f 1 $fbsplit | parallel --memfree 2G --delay 1 --jobs 0 "freebayes -f ${index_path}/genome.fa --min-mapping-quality 0 --min-base-quality 20 --min-coverage 10 --min-alternate-fraction 0.01 -C 3 --use-best-n-alleles 3 -r {} ${bamlist} > fb.{}.vcf"
vcf-concat fb.*.vcf | vcf-sort | vcf-annotate -n --fill-type | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.fb.vcf.gz -
elif [[ $algo == 'platypus' ]]
then
@@ -143,7 +143,15 @@ then
opt=''
if [[ -n $tbed ]]
then
- opt="--callRegions ${tbed}.gz"
+ if [[ -f "${tbed}.gz" ]]
+ then
+ opt="--callRegions ${tbed}.gz"
+ else
+ cp $tbed panel.bed
+ bgzip panel.bed
+ tabix panel.bed.gz
+ opt="--callRegions panel.bed.gz"
+ fi
fi
if [[ $rna == 1 ]]
then
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index dcfce30..94d4ece 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -103,14 +103,14 @@ then
opt=''
if [[ -n $tbed ]]
then
- if [[ -f $tbed ]]
+ if [[ -f "${tbed}.gz" ]]
then
opt="--callRegions ${tbed}.gz"
else
- cp $tbed targetpanel.bed
- bgzip targetpanel.bed
- tabix targetpanel.bed.gz
- opt="--callRegions targetpanel.bed.gz"
+ cp $tbed panel.bed
+ bgzip panel.bed
+ tabix panel.bed.gz
+ opt="--callRegions panel.bed.gz"
fi
fi
mkdir manta
--
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