From 2d64c49435cbc5f12e9c56de9b903d456c02ac02 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 18 Mar 2020 10:23:45 -0500
Subject: [PATCH] pindel filtering path relative to process scripts
---
variants/svcalling.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index f5b585e..7ed1734 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -157,8 +157,8 @@ then
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} ${pair_id}.sv.vcf | bgzip > ${pair_id}.pindel_sv.vcf.gz
if [[ $filter == 1 ]]
then
- perl $baseDir/process_scripts/variants/filter_pindel.pl -d ${pair_id}.pindel_tandemdup.vcf.gz -s ${pair_id}.pindel_sv.vcf.gz -i ${pair_id}.pindel_indel.vcf.gz
- mv ${pair_id}x.pindel_tandemdup.vcf.gz ${pair_id}.pindel_tandemdup.unfilt.vcf.gz
+ perl $baseDir/filter_pindel.pl -d ${pair_id}.pindel_tandemdup.vcf.gz -s ${pair_id}.pindel_sv.vcf.gz -i ${pair_id}.pindel_indel.vcf.gz
+ mv ${pair_id}.pindel_tandemdup.vcf.gz ${pair_id}.pindel_tandemdup.unfilt.vcf.gz
mv ${pair_id}.pindel_tandemdup.pass.vcf ${pair_id}.pindel_tandemdup.vcf
bgzip ${pair_id}.pindel_tandemdup.vcf
mv ${pair_id}.pindel_indel.pass.vcf ${pair_id}.pindel.vcf
--
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