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