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.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
\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 2011-2023 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.