From 21ae1046c4243577f30b80ca7c3eabb562ca1987 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 7 Oct 2020 11:01:34 -0500
Subject: [PATCH] account for LOH in CNVKit
---
variants/filter_cnvkit.pl | 48 +++++++++++++++++++++++----------------
1 file changed, 29 insertions(+), 19 deletions(-)
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index 7a87800..4829d4a 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -102,26 +102,36 @@ while (my $line = <IN>) {
print CNSO join("\t",$hash{chromosome},$hash{start},$hash{end},
$hash{log2},$hash{cn}),"\n";
- next if ($hash{cn} == 2) || scalar(keys %genes) < 1;
+ next if ($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';
- $abtype = 'loss' if ($hash{cn} < 2);
- $abtype = 'gain' if ($hash{cn} > 2 && $hash{cn} < 6);
- foreach $gene (keys %genes) {
- my @cytoband;
- if ($cyto{$key}{'p'}) {
- @nums = sort {$b <=> $a} @{$cyto{$key}{'p'}};
- push @cytoband, 'p'.$nums[0],'p'.$nums[-1];
- } if ($cyto{$key}{'q'}) {
- @nums = sort {$a <=> $b} @{$cyto{$key}{'q'}};
- push @cytoband, 'q'.$nums[0],'q'.$nums[-1];
- }
- if ($cytoband[0] eq $cytoband[-1]) {
- $cband = $cytoband[0];
- }else {
- $cband = join("-",$cytoband[0],$cytoband[-1]);
+ if ($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)) {
+ $abtype.= ' LOH';
}
- print OUT join("\t",$gene,$hash{chromosome},$hash{start},$hash{end},
- $abtype,$hash{cn},$hash{weight},$cband),"\n";
+ }
+ }else {
+ $abtype = 'cnLOH';
}
-}
+ foreach $gene (keys %genes) {
+ my @cytoband;
+ if ($cyto{$key}{'p'}) {
+ @nums = sort {$b <=> $a} @{$cyto{$key}{'p'}};
+ push @cytoband, 'p'.$nums[0],'p'.$nums[-1];
+ } if ($cyto{$key}{'q'}) {
+ @nums = sort {$a <=> $b} @{$cyto{$key}{'q'}};
+ push @cytoband, 'q'.$nums[0],'q'.$nums[-1];
+ }
+ if ($cytoband[0] eq $cytoband[-1]) {
+ $cband = $cytoband[0];
+ }else {
+ $cband = join("-",$cytoband[0],$cytoband[-1]);
+ }
+ print OUT join("\t",$gene,$hash{chromosome},$hash{start},$hash{end},
+ $abtype,$hash{cn},$hash{weight},$cband),"\n";
+ }
+ }
close IN;
--
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