From 885de9b172e722d719518bdcdfc5a633c36f91b5 Mon Sep 17 00:00:00 2001
From: Cyriac Kandoth <ckandoth@gmail.com>
Date: Wed, 16 Mar 2016 16:31:25 -0400
Subject: [PATCH] Hotfix for wrong GT in vcf2vcf

---
 vcf2vcf.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcf2vcf.pl b/vcf2vcf.pl
index 32cae9d..707d69d 100644
--- a/vcf2vcf.pl
+++ b/vcf2vcf.pl
@@ -148,7 +148,7 @@
 
         # Standardize AD and DP based on data in the genotype fields
         FixAlleleDepths( \@alleles, $var_allele_idx, \%nrm_info );
-        $tum_info{GT} = "./." unless( defined $tum_info{GT} and $tum_info{GT} ne '.' );
+        $nrm_info{GT} = "./." unless( defined $nrm_info{GT} and $nrm_info{GT} ne '.' );
     }
 
     # Add more filter tags to the FILTER field, if --add-filters was specified