From cd03f58a78dc6f9d7ae90218c0128a4c230f638e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 1 May 2020 16:17:59 -0500
Subject: [PATCH] update svaba for multiple tumor files
---
variants/svcalling.sh | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 0c3b97d..b737b98 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -110,7 +110,11 @@ then
then
svaba run -p $NPROC -G ${reffa} -t ${sbam} -n ${normal} -a ${pair_id}
else
- svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id}
+ bamlist=''
+ for i in *.bam; do
+ bamlist="$bamlist -t ${i}"
+ done
+ svaba run -p $NPROC -G ${reffa} -a ${pair_id} $bamlist
fi
#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
--
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