VCF-COMPARE(1)							   User Commands						    VCF-COMPARE(1)

vcf-compare - compare bgzipped and tabix indexed VCF files SYNOPSIS
compare-vcf [OPTIONS] file1.vcf file2.vcf ... DESCRIPTION
About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz) OPTIONS
-c, --chromosomes <list|file> Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future. -d, --debug Debugging information. Giving the option multiple times increases verbosity -H, --cmp-haplotypes Compare haplotypes, not only positions -m, --name-mapping <list|file> Use with -H when comparing files with differing column names. The argument to this options is a comma-separated list or one mapping per line in a file. The names are colon separated and must appear in the same order as the files on the command line. -R, --refseq <file> Compare the actual sequence, not just positions. Use with -w to compare indels. -r, --regions <list|file> Process the given regions (comma-separated list or one region per line in a file). -s, --samples <list> Process only the listed samples. Excluding unwanted samples may increase performance considerably. -w, --win <int> In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a SNP or an indel). -h, -?, --help This help message. vcf-compare 0.1.5 July 2011 VCF-COMPARE(1)

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