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.\" Automatically generated by Pandoc 2.7.3
.\"
.TH "VCFGENO2HAPLO" "1" "" "vcfgeno2haplo (vcflib)" "vcfgeno2haplo (VCF
transformation)"
.hy
.SH NAME
.PP
\f[B]vcfgeno2haplo\f[R]
.SH SYNOPSIS
.PP
\f[B]vcfgeno2haplo\f[R] options []
.SH DESCRIPTION
.PP
Convert genotype-based phased alleles within \[en]window-size into
haplotype alleles.
Will break haplotype construction when encountering non-phased genotypes
on input.
.SH OPTIONS
.IP
.nf
\f[C]
options:
-h, --help Print this message
-v, --version Print version
-r, --reference FILE FASTA reference file
-w, --window-size N Merge variants at most this many bp apart (default 30)
-o, --only-variants Don\[aq]t output the entire haplotype, just concatenate
REF/ALT strings (delimited by \[dq]:\[dq])
Type: transformation
\f[R]
.fi
.SH EXIT VALUES
.TP
.B \f[B]0\f[R]
Success
.TP
.B \f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2020 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.
|
