From 8f60c619b983dffa337c9aeefba98a33413dcb09 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 16 Jul 2018 11:37:11 -0500
Subject: [PATCH] add gt info virmid
---
variants/addgt_virmid.pl | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/variants/addgt_virmid.pl b/variants/addgt_virmid.pl
index ba62bb3..11cbf90 100755
--- a/variants/addgt_virmid.pl
+++ b/variants/addgt_virmid.pl
@@ -17,6 +17,15 @@ while (my $line = <VCF>) {
}else {
my ($chrom, $pos,$id,$ref,$alt,$score,
$filter,$annot) = split(/\t/, $line);
- print OUT join("\t",$line,'GT','0/0','0/1'),"\n";
+ foreach $a (split(/;/,$annot)) {
+ my ($key,$val) = split(/=/,$a);
+ $hash{$key} = $val;
+ }
+ $normalgt=join(":",'0/0',$hash{NDP},$hash{NAC},$hash{NDP}-$hash{NAC},
+ join(',',$hash{NDP}-$hash{NAC},$hash{NAC}));
+ $tumorgt=join(":",'0/0',$hash{DDP},$hash{DAC},$hash{DDP}-$hash{DAC},
+ join(',',$hash{DDP}-$hash{DAC},$hash{DAC}));
+ print OUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,
+ 'GT:DP:AO:RO:AD',$normalgt,$tumorgt),"\n";
}
}
--
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