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 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS¶

Erik Garrison and vcflib contributors.