hapLrt

       Erik Garrison and vcflib contributors.

hapLrt (vcflib)                                                                                        HAPLRT(1)

       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).

0      Success

       not0  Failure

       Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.  MIT licensed.   Copyright  2020-2024  (C)
       Pjotr Prins.

hapLrt

              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

vcflib(1)

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