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.\" Automatically generated by Pandoc 2.7.3
.\"
.TH "PLOTHAPS" "1" "" "plotHaps (vcflib)" "plotHaps (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]plotHaps\f[R]
.SH SYNOPSIS
.SH DESCRIPTION
.PP
\f[B]plotHaps\f[R] provides the formatted output that can be used with
`bin/plotHaplotypes.R'.
.SH OPTIONS
.IP
.nf
\f[C]
Output : haplotype matrix and positions
**plotHaps** --target 0,1,2,3,4,5,6,7 --file my.phased.vcf.gz
required: t,target -- argument: a zero base comma separated list of target individuals corrisponding to VCF column s
required: r,region -- argument: a tabix compliant genomic range : \[dq]seqid:start-end\[dq] or \[dq]seqid\[dq]
required: f,file -- argument: proper formatted phased VCF file
required: y,type -- argument: genotype likelihood format: PL,GP,GP
Type: statistics
\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.
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