MELTEHH(1)

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

AUTHORS
Erik Garrison and vcflib contributors.