This is the command vcf-compare that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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