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Fixed bug that required users to use the recordOriginalLocation option 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4944 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-01-05 23:12:14 +00:00
parent 5e9a8f9cb3
commit 48772a9d01
1 changed files with 2 additions and 2 deletions
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4
perl/liftOverVCF.pl
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@ -12,7 +12,7 @@ my $newRef = undef;
my $oldRef = undef;
my $out = undef;
my $tmp = "/tmp";
my $recordOriginalLocation = undef;
my $recordOriginalLocation = 0;
GetOptions( "vcf=s" => \$in,
"gatk=s" => \$gatk,
"chain=s" => \$chain,
@ -22,7 +22,7 @@ GetOptions( "vcf=s" => \$in,
"tmp=s" => \$tmp,
"recordOriginalLocation" => \$recordOriginalLocation);
if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out || !defined($recordOriginalLocation)) {
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\t-recordOriginalLocation \t\t<Should we record what the original location was in the INFO field?; defaults to false>\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);