From 3d9705fc1f42b77ce4176c04c78f067419afc704 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 30 Mar 2020 15:01:47 -0500
Subject: [PATCH] update filter cnvkit
---
variants/filter_cnvkit.pl | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index a30aeb1..86545f5 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -56,7 +56,8 @@ while (my $line = <CNR>) {
foreach my $gid (@ids) {
next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion/);
my ($gene,@other) = split(/:/,$gid);
- $genes{$gene} = 1;
+ my ($gname,@loc) = split(/_/,$gene);
+ $genes{$gname} = 1;
}
}
foreach $gene (keys %genes) {
@@ -94,7 +95,8 @@ while (my $line = <IN>) {
foreach my $gid (@ids) {
next if ($gid =~ /^rs\d+$|^SNP:rs\d+$|^-$|Fusion/);
my ($gene,@other) = split(/:/,$gid);
- $genes{$gene} = 1;
+ my ($gname,@loc) = split(/_/,$gene);
+ $genes{$gname} = 1;
}
}
my $len = sprintf("%.1f",($hash{end}-$hash{start})/1000);
--
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