normalize-iHS.md

% NORMALIZE-IHS(1) normalize-iHS (vcflib) | normalize-iHS (VCF genotype) % Erik Garrison and vcflib contributors

NAME

normalize-iHS

SYNOPSIS

normalizeHS -s 0.01 -f input.txt

DESCRIPTION

normalizes iHS or XP-EHH scores.

OPTIONS

A cross-population extended haplotype homozygosity (XP-EHH) score is
directional: a positive score suggests selection is likely to have
happened in population A, whereas a negative score suggests the same
about population B. See for example
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687721/


Output : **normalize-iHS** adds one additional column to input (normalized score).
required: -f            -- Output from iHS or XPEHH 
optional: -s            -- Max AF diff for window [0.01]

Type: genotype

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

normalize-iHS.cpp

LICENSE

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