From c313fc8ca3d92e0505b5b92897890470bb647d84 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 12 Mar 2020 15:26:55 -0500
Subject: [PATCH] svcalling svaba filtering error AD->AO
---
variants/svcalling.sh | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 25c8cb9..f5b585e 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -11,7 +11,7 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :r:p:b:i:x:y:n:l:f:a:h opt
+while getopts :r:p:b:i:x:y:n:l:a:hf opt
do
case $opt in
r) index_path=$OPTARG;;
@@ -60,7 +60,7 @@ fi
source /etc/profile.d/modules.sh
module load htslib/gcc/1.8 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14
export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
-mkdir temp
+mkdir -p temp
if [[ $method == 'delly' ]]
then
@@ -106,7 +106,7 @@ then
#Create SV FILE
vcf-concat ${pair_id}.svaba.unfiltered*sv.vcf | perl -pe 's/\.consensus|\.bam//g' | vcf-sort| bgzip > ${pair_id}.svaba.unfiltered.sv.vcf.gz
bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.sv -v ${pair_id}.svaba.unfiltered.sv.vcf.gz
- java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].AD >= 20)" | bgzip > ${pair_id}.svaba.sv.vcf.gz
+ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].AO >= 20)" | bgzip > ${pair_id}.svaba.sv.vcf.gz
vcf-concat ${pair_id}.svaba.unfiltered*indel.vcf | perl -pe 's/\.consensus|\.bam//g' | vcf-sort | java -jar $SNPEFF_HOME/SnpSift.jar filter "( SPAN >= 20)" - |bgzip > ${pair_id}.svaba.indel.vcf.gz
bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.indel -v ${pair_id}.svaba.indel.vcf.gz
--
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