From d2eb7063a5b6d90cf69dcecdd03da5ea1f12da82 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 20 Dec 2018 21:09:28 -0600
Subject: [PATCH] updates alt/ref pindel
---
variants/parse_pindel.pl | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/variants/parse_pindel.pl b/variants/parse_pindel.pl
index facbeff..79c0e23 100755
--- a/variants/parse_pindel.pl
+++ b/variants/parse_pindel.pl
@@ -77,14 +77,15 @@ while (my $line = <VCF>) {
next if ($missingGT == scalar(@gts));
if ($hash{SVTYPE} eq 'DUP:TANDEM') {
- print DUP join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
+ print DUP join("\t",$chrom,$pos,$id,'N','<DUP>',$score,$filter,$annot,$newformat,@newgts),"\n";
}elsif ($hash{SVTYPE} eq 'INS') {
- print SV join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
+ print SV join("\t",$chrom,$pos,$id,'N','<INS>',$score,$filter,$annot,$newformat,@newgts),"\n";
}elsif ($hash{SVTYPE} eq 'DEL' || $hash{SVTYPE} eq 'INS') {
if (abs($hash{SVLEN}) < 50) {
print SI join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
}else {
- print SV join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
+ $newalt = "<".$hash{SVTYPE}.">";
+ print SV join("\t",$chrom,$pos,$id,'N',$newalt,$score,$filter,$annot,$newformat,@newgts),"\n";
}
}
}
--
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