diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh index c143ea31bb20bb6e1ee5c60fac3c7b52743228e2..014d0206823040d95a34038b974a4d3820f54379 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 ]]