HAPLRT

NAME

hapLrt

SYNOPSIS

hapLRT –target 0,1,2,3,4,5,6,7 –background 11,12,13,16,17,19,22 –type GP –file my.vcf

DESCRIPTION

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).

OPTIONS

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 or GP
optional: r,region -- argument: a genomic range to calculate **hapLrt** on in the format : "seqid:start-end" or "seqid"

Type: genotype

EXIT VALUES

	0		Success
	not 0		Failure

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS

Erik Garrison and vcflib contributors.