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 2011-2025 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2025 (C) Pjotr Prins.

AUTHORS

Erik Garrison and vcflib contributors.