VCFSTATS(1)

NAME

vcfstats

SYNOPSIS

vcfstats options

DESCRIPTION

Prints statistics about variants in the input VCF file.

OPTIONS

        -r, --region          specify a region on which to target the stats, requires a BGZF
                              compressed file which has been indexed with tabix.  any number of
                              regions may be specified.
        -a, --add-info        add the statistics intermediate information to the VCF file,
                              writing out VCF records instead of summary statistics
        -t, --add-type        only add the type= field to the info (faster than -a)
        -l, --no-length-frequency    don't out the indel and mnp length-frequency spectra
        -m, --match-score N          match score for SW algorithm
        -x, --mismatch-score N       mismatch score for SW algorithm
        -o, --gap-open-penalty N     gap open penalty for SW algorithm
        -e, --gap-extend-penalty N   gap extension penalty for SW algorithm
    Type: statistics

EXIT VALUES

0   Success

not 0
    Failure

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS
Erik Garrison and vcflib contributors.