From ad5b87f99ce352066805ed352f52d90507ffdce3 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 19 Oct 2018 15:12:07 -0500
Subject: [PATCH] update union.sh
---
variants/unionvcf.pl | 60 +++++++++++++++++++++++---------------------
1 file changed, 31 insertions(+), 29 deletions(-)
diff --git a/variants/unionvcf.pl b/variants/unionvcf.pl
index ee84efb..57c2046 100755
--- a/variants/unionvcf.pl
+++ b/variants/unionvcf.pl
@@ -118,7 +118,7 @@ foreach $vcf (@vcffiles) {
push @gtdesc, join(":",$id,$afinfo{$id});
push @newgts, $newgts{$id};
}
- $lines{$chrom}{$pos}{$caller} = [$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,\@newgts,\@gtdesc];
+ $lines{$chrom}{$pos}{$alt}{$caller} = [$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,\@newgts,\@gtdesc];
}
close VCF;
}
@@ -128,37 +128,39 @@ if (grep(/mutect/,@vcffiles)) {
}
F1:foreach $chr (sort {$a cmp $b} keys %lines) {
F2:foreach $pos (sort {$a <=> $b} keys %{$lines{$chr}}) {
- my @callset;
- my %csets;
- F3:foreach $caller (sort {$a cmp $b} keys %{$lines{$chr}{$pos}}) {
- my ($chrom, $pos,$id,$ref,$alt,$score,$filter,$annot,
- $format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$caller}};
- @gtdesc = @{$gtdescref};
- foreach $gtd (@gtdesc) {
- my ($id,$dp,$maf) = split(/:/,$gtd);
- push @{$csets{$id}}, [$caller,$dp,$maf];
- }
- push @callset, join("|",$caller,$alt,@gtdesc);
- }
- my $consistent = 1;
- foreach $id (keys %csets) {
- my @calls = @{$csets{$id}};
- my @calls = sort {$a[2] <=> $b[2]} @calls;
- $consistent = 0 if ($calls[0][2] < 0.25 && $calls[-1][2] - $calls[0][2] > 0.10 && $calls[-1][2]/($calls[0][2]+0.001) > 3);
- }
- F3:foreach $caller (@callers) {
- if ($lines{$chr}{$pos}{$caller}) {
+ F4:foreach $alt (sort {$a <=> $b} keys %{$lines{$chr}{$pos}}) {
+ my @callset;
+ my %csets;
+ F3:foreach $caller (sort {$a cmp $b} keys %{$lines{$chr}{$pos}{$alt}}) {
my ($chrom, $pos,$id,$ref,$alt,$score,$filter,$annot,
- $format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$caller}};
- @gts = @{$gtsref};
+ $format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$alt}{$caller}};
@gtdesc = @{$gtdescref};
- $annot = $annot.";CallSet=".join(",",@callset);
- unless ($consistent) {
- $annot = $annot.";CallSetInconsistent=1";
+ foreach $gtd (@gtdesc) {
+ my ($id,$dp,$maf) = split(/:/,$gtd);
+ push @{$csets{$id}}, [$caller,$dp,$maf];
+ }
+ push @callset, join("|",$caller,$alt,@gtdesc);
+ }
+ my $consistent = 1;
+ foreach $id (keys %csets) {
+ my @calls = @{$csets{$id}};
+ my @calls = sort {$a[2] <=> $b[2]} @calls;
+ $consistent = 0 if ($calls[0][2] < 0.25 && $calls[-1][2] - $calls[0][2] > 0.10 && $calls[-1][2]/($calls[0][2]+0.001) > 3);
+ }
+ F3:foreach $caller (@callers) {
+ if ($lines{$chr}{$pos}{$alt}{$caller}) {
+ my ($chrom, $pos,$id,$ref,$alt,$score,$filter,$annot,
+ $format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$alt}{$caller}};
+ @gts = @{$gtsref};
+ @gtdesc = @{$gtdescref};
+ $annot = $annot.";CallSet=".join(",",@callset);
+ unless ($consistent) {
+ $annot = $annot.";CallSetInconsistent=1";
+ }
+ print OUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,
+ $filter,$annot,$format,@gts),"\n";
+ last F3;
}
- print OUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,
- $filter,$annot,$format,@gts),"\n";
- last F3;
}
}
}
--
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