DOKK / manpages / debian 12 / libvcflib-tools / vcfstats.1.en
VCFSTATS(1) vcfstats (VCF statistics) VCFSTATS(1)

vcfstats

vcfstats options

Prints statistics about variants in the input VCF file.



    -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

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vcflib(1)

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

Erik Garrison and vcflib contributors.

vcfstats (vcflib)