1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
|
.\" Automatically generated by Pandoc 2.19.2
.\"
.\" Define V font for inline verbatim, using C font in formats
.\" that render this, and otherwise B font.
.ie "\f[CB]x\f[]"x" \{\
. ftr V B
. ftr VI BI
. ftr VB B
. ftr VBI BI
.\}
.el \{\
. ftr V CR
. ftr VI CI
. ftr VB CB
. ftr VBI CBI
.\}
.TH "NORMALIZE-IHS" "1" "" "normalize-iHS (vcflib)" "normalize-iHS (VCF genotype)"
.hy
.SH NAME
.PP
\f[B]normalize-iHS\f[R]
.SH SYNOPSIS
.PP
normalizeHS -s 0.01 -f input.txt
.SH DESCRIPTION
.PP
normalizes iHS or XP-EHH scores.
.SH OPTIONS
.IP
.nf
\f[C]
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
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.
MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
.SH AUTHORS
Erik Garrison and vcflib contributors.
|
