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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
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ebanks 2010-10-05 13:50:24 +00:00
parent 250c18e679
commit 7f1e44b764
1 changed files with 1 additions and 1 deletions
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2
perl/liftOverVCF.pl
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@ -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);
}