From 56d7ffe2b5b6a1f1611d2a150014faab0291415d Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 12 Oct 2020 16:30:05 -0500
Subject: [PATCH] updates to filter cnvkit abberation type
---
variants/filter_cnvkit.pl | 24 +++++++++++++++---------
1 file changed, 15 insertions(+), 9 deletions(-)
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index 4829d4a..d5220ba 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -104,16 +104,22 @@ while (my $line = <IN>) {
next if ($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 '');
- my $abtype = 'amplification';
- if ($hash{cn} != 2) {
- $abtype = 'loss' if ($hash{cn} < 2);
- if ($hash{cn} > 2 && $hash{cn} < 6) {
- $abtype = 'gain' ;
- if ($hash{cn1} ne '' && $hash{cn2} ne '' && ($hash{cn1} == 0 || $hash{cn2} == 0)) {
- $abtype.= ' LOH';
- }
+ my $abtype = 'cnLOH';
+ if ($hash{cn} < 2) {
+ if ($hash{cn} < 1 ) {
+ $abtype = 'homozygous deletion';
+ }else {
+ $abtype = 'hemizygous deletion';
+ }
+ } elsif ($hash{cn} > 2) {
+ $abtype = 'gain' ;
+ if ($hash{cn} > 6) {
+ $abtype = 'amplification';
}
- }else {
+ if ($hash{cn1} ne '' && $hash{cn2} ne '' && ($hash{cn1} == 0 || $hash{cn2} == 0)) {
+ $abtype.= ' LOH';
+ }
+ } else {
$abtype = 'cnLOH';
}
foreach $gene (keys %genes) {
--
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