diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl index 083f1f5369a1c39dfb5bf92306afd3dc96513d05..6dfdf441403379f1764b4ef450c8bfb20f0ad38a 100755 --- a/variants/filter_cnvkit.pl +++ b/variants/filter_cnvkit.pl @@ -100,7 +100,12 @@ while (my $line = <IN>) { print BIO join("\t",$gene,$entrez{$gene},$cn_cbio),"\n"; print BIO2 join("\t",$gene,$entrez{$gene},$log2),"\n"; my @cytoband = sort {$a->[1] <=>$b->[1]} @{$cyto{$key}}; - print OUT2 join("\t",$gene,$chr,$start,$end,$abtype,$cn,$weight,join("",@{$cytoband[0]},'-',@{$cytoband[-1]})),"\n"; + if (join("",@{$cytoband[0]}) eq join("",@{$cytoband[-1]})) { + $cband = join("",@{$cytoband[0]}); + }else { + $cband = join("",@{$cytoband[0]},'-',@{$cytoband[-1]}); + } + print OUT2 join("\t",$gene,$chr,$start,$end,$abtype,$cn,$weight,$cband),"\n"; print OUT join("\t",$gene,$chr,$start,$end,$abtype,$cn,$weight),"\n"; } }