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.TH "VCFSTATS" "1" "" "vcfstats (vcflib)" "vcfstats (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]vcfstats\f[R]
.SH SYNOPSIS
.PP
\f[B]vcfstats\f[R] options
.SH DESCRIPTION
.PP
Prints statistics about variants in the input VCF file.
.SH OPTIONS
.IP
.nf
\f[C]
-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\[aq]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
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.
MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
.SH AUTHORS
Erik Garrison and vcflib contributors.
|
