Man page - haplrt(1)

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Package: libvcflib-tools
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libvcflib-tools

Manual

HAPLRT

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS

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, GT 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

OTHER

LICENSE

AUTHORS

Erik Garrison and vcflib contributors.