1% NORMALIZE-IHS(1) normalize-iHS (vcflib) | normalize-iHS (VCF genotype)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**normalize-iHS**
7
8# SYNOPSIS
9
10normalizeHS -s 0.01 -f input.txt
11
12# DESCRIPTION
13
14normalizes iHS or XP-EHH scores.
15
16
17
18# OPTIONS
19
20```
21
22
23
24
25A cross-population extended haplotype homozygosity (XP-EHH) score is
26directional: a positive score suggests selection is likely to have
27happened in population A, whereas a negative score suggests the same
28about population B. See for example
29https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687721/
30
31
32Output : **normalize-iHS** adds one additional column to input (normalized score).
33required: -f            -- Output from iHS or XPEHH
34optional: -s            -- Max AF diff for window [0.01]
35
36Type: genotype
37
38
39
40```
41
42
43
44
45
46# EXIT VALUES
47
48**0**
49: Success
50
51**not 0**
52: Failure
53
54# SEE ALSO
55
56
57
58[vcflib](./vcflib.md)(1)
59
60
61
62# OTHER
63
64## Source code
65
66[normalize-iHS.cpp](https://github.com/vcflib/vcflib/blob/master/src/normalize-iHS.cpp)
67
68# LICENSE
69
70Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
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