updates to cnvkit

variants/cnvkit.sh

@@ -49,7 +49,7 @@ then
 elif [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2_2.panelplus.bed' ]]
 then
     normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
-    target='panel1385V2-2.cnvkit_'
+    targets="${index_path}/panel1385V2-2.cnvkit_"
 fi
 
 echo "${targets}targets.bed"

variants/filter_cnvkit.pl

@@ -73,7 +73,7 @@ while (my $line = <CNR>) {
 }
 
 open IN, "<$file" or die $!;
-my $header = <IN>;
+$header = <IN>;
 while (my $line = <IN>) {
     chomp($line);
     my ($chr,$start,$end,$geneids,$log2,$cn,$depth,