vcf-compare: Compare bgzipped and tabix indexed vcf files

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.