From f29af9013c809e6d0050d4049a9a51c7f6cbb116 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 28 Feb 2018 11:05:25 -0600
Subject: [PATCH] update cnv kit filter
---
variants/filter_cnvkit.pl | 10 ++++------
1 file changed, 4 insertions(+), 6 deletions(-)
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index ad18cc1..cbd46a3 100644
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -18,9 +18,8 @@ while (my $line = <ENT_ENS>){
}
close ENT_ENS;
open ENT_SYM, "</project/shared/bicf_workflow_ref/gene_info.human.txt" or die $!;
-my %entrez;
-my $ent_header = <ENT_ENS>;
-while (my $line = <ENT_ENS>){
+$ent_header = <ENT_SYM>;
+while (my $line = <ENT_SYM>){
chomp $line;
my @row = split(/\t/, $line);
$entrez{$row[2]}=$row[1];
@@ -49,17 +48,16 @@ while (my $line = <IN>) {
$genes{$value} = 1 if $keep{$value};
}
}
- my $newgeneids = join(";", keys %genes);
my $len = sprintf("%.1f",($end-$start)/1000);
next if ($cn == 2) || scalar(keys %genes) < 1;
my $abtype = 'amplification';
$abtype = 'loss' if ($cn < 2);
- foreach $gene (keys %gene) {
+ foreach $gene (keys %genes) {
$cn_cbio = $cn -2;
$cn_cbio = 2 if ($cn > 4);
print BIO join("\t",$gene,$entrez{$gene},$cn_cbio),"\n";
+ print OUT join("\t",$gene,$chr,$start,$end,$abtype,$cn,$weight),"\n";
}
- print OUT join("\t",$newgeneids,$chr,$start,$end,$abtype,$cn,$weight),"\n";
}
close IN;
close OUT;
--
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