cnvkit no removal of chrX copy 1; starfusion Jeremy fixes

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

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;