From 7f1e44b764ccaeaf5eeaab5e885c9aa0a07b3ad9 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 5 Oct 2010 13:50:24 +0000
Subject: [PATCH] update the example: /broad/1KG doesn't exist anymore

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4429 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 e06dbf641..e02ba98a8 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -22,7 +22,7 @@ GetOptions( "vcf=s" => \$in,
 
 if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out ) {
     print "Usage: liftOverVCF.pl\n\t-vcf \t\t<input vcf>\n\t-gatk \t\t<path to gatk trunk>\n\t-chain \t\t<chain file>\n\t-newRef \t<path to new reference prefix; we will need newRef.dict, .fasta, and .fasta.fai>\n\t-oldRef \t<path to old reference prefix; we will need oldRef.fasta>\n\t-out \t\t<output vcf>\n\t-tmp \t\t<temp file location; defaults to /tmp>\n";
-    print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /broad/1KG/reference/human_b36_both\n";
+    print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /humgen/1kg/reference/human_b36_both\n";
     exit(1);
 }