From 87557454d9e6bf49ff5333418e23579ed3753e07 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 20 Nov 2017 16:22:08 -0600
Subject: [PATCH] update unioncode platypus bug
---
variants/unionvcf.pl | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/variants/unionvcf.pl b/variants/unionvcf.pl
index 6329433..277855f 100755
--- a/variants/unionvcf.pl
+++ b/variants/unionvcf.pl
@@ -24,12 +24,16 @@ foreach $vcf (@vcffiles) {
if ($line =~ m/#CHROM/) {
($chromhd, $posd,$idhd,$refhd,$althd,$scorehd,
$filterhd,$annothd,$formathd,@sampleids) = split(/\t/, $line);
+ foreach $j (0..$#sampleids) {
+ $sampleids[$j] =~ s/\.final//g;
+ }
unless (@sampleorder) {
@sampleorder = @sampleids;
print OUT $line,"\n";
}
next;
}
+ next;
}
my ($chrom, $pos,$id,$ref,$alt,$score,
$filter,$annot,$format,@gts) = split(/\t/, $line);
@@ -55,7 +59,7 @@ foreach $vcf (@vcffiles) {
foreach my $i (0..$#deschead) {
$gtdata{$deschead[$i]} = $gtinfo[$i];
}
- if ($gtdata{DP} == 0 || $gtdata{GT} eq './.') {
+ if ($gtdata{GT} eq './.') {
$newgts{$sid} = '.:.:.:.:.';
$missingGT ++;
next FG;
@@ -71,6 +75,7 @@ foreach $vcf (@vcffiles) {
$gtdata{DP} = $gtdata{NR};
$gtdata{AO} = $gtdata{NV};
$gtdata{RO} = $gtdata{DP} - $gtdata{AO};
+ $gtdata{AD} = join(",",$gtdata{RO},$gtdata{AO})
} elsif (exists $gtdata{AO} && exists $gtdata{RO}) {
$gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
$gtdata{DP} = $gtdata{RO};
--
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