Man page - vcf-compare(1)
Packages contains this manual
- vcf-query(1)
- vcf-stats(1)
- vcf-to-tab(1)
- vcf-concat(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-phased-join(1)
- fill-aa(1)
- vcf-isec(1)
- vcf-consensus(1)
- vcf-tstv(1)
- vcf-merge(1)
- vcf-subset(1)
- vcf-contrast(1)
- vcf-fix-newlines(1)
- fill-an-ac(1)
- vcftools(1)
- vcf-validator(1)
- fill-fs(1)
- vcf-fix-ploidy(1)
- vcf-compare(1)
- fill-ref-md5(1)
- vcf-annotate(1)
- vcf-convert(1)
- vcf-shuffle-cols(1)
apt-get install vcftools
Manual
VCF-COMPARE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
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.