vcf-compare(1)
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.