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% MELTEHH(1) meltEHH (vcflib) | meltEHH (VCF statistics) % Erik Garrison and vcflib contributors

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

Source code

meltEHH.cpp

LICENSE

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