From cabc31902db3374b96a90e98a9044a135b5329eb Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 19 Sep 2019 15:58:12 -0500
Subject: [PATCH] update strelka2 somatic depth info
---
variants/uniform_vcf_gt.pl | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/variants/uniform_vcf_gt.pl b/variants/uniform_vcf_gt.pl
index 6c894c0..fd497db 100755
--- a/variants/uniform_vcf_gt.pl
+++ b/variants/uniform_vcf_gt.pl
@@ -59,6 +59,16 @@ while (my $line = <VCF>) {
foreach (split(',',$gtdata{AO})) {
$gtdata{DP} += $_;
}
+ } elsif ($gtdata{TIR}) {
+ $gtdata{GT} = '0/0';
+ $gtdata{AO} = (split(/,/,$gtdata{TIR}))[0];
+ $gtdata{RO} = $gtdata{DP} - $gtdata{AO};
+ $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
+ } elsif ($gtdata{$ref."U"} && $gtdata{$alt."U"}) {
+ $gtdata{GT} = '0/0';
+ $gtdata{AO} = (split(/,/,$gtdata{$alt."U"}))[0];
+ $gtdata{RO} = (split(/,/,$gtdata{$ref."U"}))[0];
+ $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
}
if ($gtdata{DP} && $gtdata{DP} < 5) {
$missingGT ++;
--
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