CrossMap.py vcf <chain_file> <input.vcf> <refGenome.fa> <output_file> [options] Examples: CrossMap.py vcf hg19ToHg18.over.chain.gz test.hg19.vcf hg18.fa test.hg18.vcf # comparing ref_allele to alt_allele to make sure they are different. CrossMap.py vcf hg19ToHg18.over.chain.gz test.hg19.vcf hg18.fa test.hg18.vcf --no-comp-alleles #do NOT compare ref_allele to alt_allele. Options: --no-comp-a