From a7af605d95e674c95a1da6bc62027e298a26e0b6 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Aug 2010 20:21:53 +0000
Subject: [PATCH] update to use new rod syntax

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4119 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/liftOverVCF.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl
index f0934b9ca..e06dbf641 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -34,7 +34,7 @@ my $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
 
 # lift over the file
 print "Lifting over the vcf...";
-my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B variant,vcf,$in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
+my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
 system($cmd);
 
 # we need to sort the lifted over file now
@@ -61,7 +61,7 @@ close(SORTED);
 
 # Filter the VCF for bad records
 print "\nFixing/removing bad records...\n";
-$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B variant,vcf,$sorted_vcf -o $out";
+$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $sorted_vcf -o $out";
 system($cmd);
 
 # clean up