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.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 corresponding to VCF columns        
required: b,background -- argument: a zero base comma separated list of background individuals corresponding to VCF columns    
required: f,file       -- argument: a properly formatted phased VCF file                                                       
required: y,type       -- argument: type of genotype likelihood: PL, GL, GT or GP                                                  
optional: r,region     -- argument: a genomic 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
\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.