From e5e905a0ada2d2a93ff0ed59b2fdf022a56c7464 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 19 Oct 2020 15:13:35 -0500
Subject: [PATCH] updates cn definitions
---
variants/filter_cnvkit.pl | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index d5220ba..6bd10c2 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -102,8 +102,12 @@ while (my $line = <IN>) {
print CNSO join("\t",$hash{chromosome},$hash{start},$hash{end},
$hash{log2},$hash{cn}),"\n";
- next if ($hash{cn} == 2 && $hash{cn1} ne '' && $hash{cn2} ne '' && $hash{cn1} > 0 && $hash{cn2} > 0) || scalar(keys %genes) < 1;
- next if ($hash{cn} == 2 && $hash{cn1} eq '' && $hash{cn2} eq '');
+ if (exists $hash{cn1} && exists $hash{cn2}) {
+ next if (($hash{cn} == 2 && $hash{cn1} ne '' && $hash{cn2} ne '' && $hash{cn1} > 0 && $hash{cn2} > 0) || scalar(keys %genes) < 1);
+ next if ($hash{cn} == 2 && $hash{cn1} eq '' && $hash{cn2} eq '');
+ }else {
+ next if ($hash{cn} == 2 || scalar(keys %genes) < 1);
+ }
my $abtype = 'cnLOH';
if ($hash{cn} < 2) {
if ($hash{cn} < 1 ) {
@@ -116,8 +120,10 @@ while (my $line = <IN>) {
if ($hash{cn} > 6) {
$abtype = 'amplification';
}
- if ($hash{cn1} ne '' && $hash{cn2} ne '' && ($hash{cn1} == 0 || $hash{cn2} == 0)) {
- $abtype.= ' LOH';
+ if (exists $hash{cn1} && exists $hash{cn2}) {
+ if ($hash{cn1} ne '' && $hash{cn2} ne '' && ($hash{cn1} == 0 || $hash{cn2} == 0)) {
+ $abtype.= ' LOH';
+ }
}
} else {
$abtype = 'cnLOH';
--
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