diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl index a2d7aa91d..a03a4fe16 100755 --- a/perl/liftOverVCF.pl +++ b/perl/liftOverVCF.pl @@ -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\n\t-gatk \t\t\n\t-chain \t\t\n\t-newRef \t\n\t-oldRef \t\n\t-out \t\t\n\t-tmp \t\t\n\t-recordOriginalLocation \t\t\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);