From eca14a2f3626da97234fcbf8867f75f7e453469c Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 19 Sep 2019 13:43:31 -0500
Subject: [PATCH] fix sname pindel
---
variants/pindel.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/variants/pindel.sh b/variants/pindel.sh
index 81b53a5..452d258 100755
--- a/variants/pindel.sh
+++ b/variants/pindel.sh
@@ -50,7 +50,7 @@ genomefiledate=`find ${reffa} -maxdepth 0 -printf "%TY%Tm%Td\n"`
module load samtools/1.6 pindel/0.2.5-intel snpeff/4.3q bedtools/2.26.0
touch ${pair_id}.pindel.config
for i in *.bam; do
- sname="${i%.bam}"
+ sname=`echo "$i" |cut -f 1 -d '.'`
echo -e "${i}\t400\t${sname}" >> ${pair_id}.pindel.config
done
--
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