VCFSTATS

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

AUTHORS

Erik Garrison and vcflib contributors.