From 3776538bd1c0cae133937145cb3e5499910fc55f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 24 Jul 2020 17:01:39 -0500
Subject: [PATCH] update starfusion/agfusion 95
---
alignment/starfusion.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index c143ea3..014d020 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -60,7 +60,7 @@ else
refgeno=${index_path}/CTAT_resource_lib
STAR-Fusion --genome_lib_dir ${refgeno} --min_sum_frags 3 --left_fq ${fq1} --right_fq ${fq2} --output_dir ${pair_id}_star_fusion &> star_fusion.err
cp ${pair_id}_star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
- cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "agfusion annotate -db agfusion.homo_sapiens.87.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
+ cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "agfusion annotate -db agfusion.homo_sapiens.95.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
fi
if [[ $filter == 1 ]]
--
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