NAME

       meltEHH

SYNOPSIS

       meltEHH –target 0,1,2,3,4,5,6,7 –pos 10 –file my.phased.vcf  –region chr1:1-1000 > STDOUT 2> STDERR

DESCRIPTION

OPTIONS

               **meltEHH** provides the data to plot extended haplotype homozygosity
              (EHH) curves and produces the data to generate the following plot:
              <img src="https://github.com/vcflib/vcflib/blob/master/examples/example-ehh.png?raw=true" alt="" width=400>

                   **meltEHH** provides the data to plot EHH curves.
              Output : 4 columns :
                   1. seqid
                   2. position
                   3. EHH
                   4. ref or alt [0 == ref]
              Params:
                     required: t,target   <STRING>  A zero base comma separated list of target
                                                   individuals corresponding to VCF columns
                     required: r,region   <STRING>  A tabix compliant genomic range
                                                   format: "seqid:start-end" or "seqid"
                     required: f,file     <STRING>  Proper formatted and phased VCF.
                     required: y,type     <STRING>  Genotype likelihood format: GT,PL,GL,GP
                     required: p,position <INT>     Variant position to melt.
                     optional: a,af       <DOUBLE>  Alternative alleles with frequencies less
                                                   than [0.05] are skipped.

              Type: statistics

EXIT VALUES

       0      Success

       not 0  Failure

SEE ALSO

       vcflib(1)

OTHER

LICENSE

       Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.  MIT licensed.

AUTHORS

       Erik Garrison and vcflib contributors.

meltEHH (vcflib)                                                                                      MELTEHH(1)