From e3b7d3bd2a7d91a312cff1fd1d41686d2c6dbf9b Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 15 Jul 2020 10:33:27 -0500
Subject: [PATCH] cnvkit no removal of chrX copy 1; starfusion Jeremy fixes
---
alignment/starfusion.sh | 11 +++++++----
variants/filter_cnvkit.pl | 1 -
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index a9f984c..c5c206f 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -53,17 +53,20 @@ then
refgeno=${index_path}/CTAT_lib_trinity1.6
trinity /usr/local/src/STAR-Fusion/STAR-Fusion --min_sum_frags 3 --CPU $NPROC --genome_lib_dir ${refgeno} --left_fq ${fq1} --right_fq ${fq2} --examine_coding_effect --output_dir ${pair_id}_star_fusion
cp ${pair_id}_star_fusion/star-fusion.fusion_predictions.abridged.coding_effect.tsv ${pair_id}.starfusion.txt
+ module load singularity/3.0.2
+ export PYENSEMBL_CACHE_DIR="/project/shared/bicf_workflow_ref/singularity_images"
+ cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "singularity exec /project/shared/bicf_workflow_ref/singularity_images/agfusion.simg agfusion annotate -db /project/shared/bicf_workflow_ref/singularity_images/pyensembl/GRCh38/ensembl92/agfusion.homo_sapiens.92.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
else
+ #jeremy to change for DNANEXUS
module add star/2.5.2b
refgeno=${index_path}/CTAT_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
+ module load singularity/3.0.2
+ export PYENSEMBL_CACHE_DIR="/project/shared/bicf_workflow_ref/singularity_images"
+ cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "singularity exec /project/shared/bicf_workflow_ref/singularity_images/agfusion.simg agfusion annotate -db /project/shared/bicf_workflow_ref/singularity_images/pyensembl/GRCh38/ensembl92/agfusion.homo_sapiens.92.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
fi
-module load singularity/3.0.2
-export PYENSEMBL_CACHE_DIR="/project/shared/bicf_workflow_ref/singularity_images"
-cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "singularity exec /project/shared/bicf_workflow_ref/singularity_images/agfusion.simg agfusion annotate -db /project/shared/bicf_workflow_ref/singularity_images/pyensembl/GRCh38/ensembl92/agfusion.homo_sapiens.92.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
-
if [[ $filter == 1 ]]
then
cut -f 6,8 ${pair_id}.starfusion.txt |grep -v Breakpoint |perl -pe 's/\t/\n/g' |awk -F ':' '{print $1"\t"$2-1"\t"$2}' > temp.bed
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index ef06a3e..7a87800 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -78,7 +78,6 @@ while (my $line = <IN>) {
foreach my $j (0..$#row) {
$hash{$colnames[$j]} = $row[$j];
}
- next if ($hash{chromosome} eq 'chrX' && $hash{cn} == 1);
my $key = $hash{chromosome}.":".$hash{start}."-".$hash{end};
my $geneids = $hash{gene};
my %genes;
--
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