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.\" Automatically generated by Pandoc 2.7.3
.\"
.TH "HAPLRT" "1" "" "hapLrt (vcflib)" "hapLrt (VCF genotype)"
.hy
.SH NAME
.PP
\f[B]hapLrt\f[R]
.SH SYNOPSIS
.PP
hapLRT \[en]target 0,1,2,3,4,5,6,7 \[en]background 11,12,13,16,17,19,22
\[en]type GP \[en]file my.vcf
.SH DESCRIPTION
.PP
HapLRT is a likelihood ratio test for haplotype lengths.
The lengths are modeled with an exponential distribution.
The sign denotes if the target has longer haplotypes (1) or the
background (-1).
.SH OPTIONS
.IP
.nf
\f[C]
Output : 4 columns :
1. seqid
2. position
3. mean target haplotype length
4. mean background haplotype length
5. p-value from LRT
6. sign
required: t,target -- argument: a zero base comma separated list of target individuals corrisponding to VCF columns
required: b,background -- argument: a zero base comma separated list of background individuals corrisponding to VCF columns
required: f,file -- argument: a properly formatted phased VCF file
required: y,type -- argument: type of genotype likelihood: PL, GL or GP
optional: r,region -- argument: a genomice range to calculate **hapLrt** on in the format : \[dq]seqid:start-end\[dq] or \[dq]seqid\[dq]
Type: genotype
\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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