From 22abbc0edbb64c093f733b91b1ad96204e0885af Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Jun 2010 13:44:03 +0000
Subject: [PATCH] Stupid cent_os doesn't allow old style 'sort' conventions. 
 Updating liftover script...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3577 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/liftOverVCF.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl
index 05ea573c1..23ff65239 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -55,7 +55,7 @@ while ( $inHeader == 1 ) {
 }
 close(UNSORTED);
 
-$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n +1 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai";
+$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai";
 print SORTED `$cmd`;
 close(SORTED);