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
77
78
79
80
81
82
|
.\" 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 "PFST" "1" "" "pFst (vcflib)" "pFst (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]pFst\f[R]
.SH SYNOPSIS
.PP
\f[B]pFst\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]pFst\f[R] is a probabilistic approach for detecting differences in
allele frequencies between two populations.
.SH OPTIONS
.IP
.nf
\f[C]
**pFst** is a likelihood ratio test (LRT) quantifying allele frequency
differences between populations. The LRT by default uses the binomial
distribution. If Genotype likelihoods are provided it uses a modified
binomial that weights each allele count by its certainty. If type is
set to \[aq]PO\[aq] the LRT uses a beta distribution to fit the allele
frequency spectrum of the target and background. PO requires the AD
and DP genotype fields and requires at least two pools for the target
and background. The p-value calculated in **pFst** is based on the
chi-squared distribution with one degree of freedom.
Output : 3 columns :
1. seqid
2. position
3. **pFst** probability
required: t,target -- argument: a zero based comma separated list of target individuals corresponding to VCF columns
required: b,background -- argument: a zero based comma separated list of background individuals corresponding to VCF columns
required: f,file -- argument: a properly formatted VCF.
required: y,type -- argument: genotype likelihood format ; genotypes: GP, GL or PL; pooled: PO
optional: d,deltaaf -- argument: skip sites where the difference in allele frequencies is less than deltaaf, default is zero
optional: r,region -- argument: a tabix compliant genomic range : seqid or seqid:start-end
optional: c,counts -- switch : use genotype counts rather than genotype likelihoods to estimate parameters, default false
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.
|
