NAME

       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.