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
70
71
72
73
74
75
76
|
.\" 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 "WCFST" "1" "" "wcFst (vcflib)" "wcFst (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]wcFst\f[R]
.SH SYNOPSIS
.PP
\f[B]wcFst\f[R] \[en]target 0,1,2,3,4,5,6,7 \[en]background
11,12,13,16,17,19,22 \[en]file my.vcf \[en]deltaaf 0.1 \[en]type PL
.SH DESCRIPTION
.PP
\f[B]wcFst\f[R] is Weir & Cockerham\[cq]s Fst for two populations.
Negative values are VALID, they are sites which can be treated as zero
Fst.
For more information see Evolution, Vol.
38 N.
6 Nov 1984.
Specifically \f[B]wcFst\f[R] uses equations 1,2,3,4.
.SH OPTIONS
.IP
.nf
\f[C]
Output : 3 columns :
1. seqid
2. position
3. target allele frequency
4. background allele frequency
5. **wcFst**
required: t,target -- argument: a zero based comma separated list of target individuals corrisponding to VCF columns
required: b,background -- argument: a zero based comma separated list of background individuals corrisponding to VCF columns
required: f,file -- argument: proper formatted VCF
required, y,type -- argument: genotype likelihood format; genotype : GT,GL,PL,GP
optional: r,region -- argument: a tabix compliant genomic range: seqid or seqid:start-end
optional: d,deltaaf -- argument: skip sites where the difference in allele frequencies is less than deltaaf, default is zero
Type: statistics
\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.
|
