vcf-compare - compare bgzipped and tabix indexed VCF files

       About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)

       vcf-compare - compare bgzipped and tabix indexed VCF files

-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)

compare-vcf [OPTIONS] file1.vcffile2.vcf ...