HAPLRT(1)

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

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2025 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2025 (C) Pjotr Prins.

AUTHORS
Erik Garrison and vcflib contributors.