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
|
% WCFST(1) wcFst (vcflib) | wcFst (VCF statistics)
% Erik Garrison and vcflib contributors
# NAME
**wcFst**
# SYNOPSIS
**wcFst** --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf --deltaaf 0.1 --type PL
# DESCRIPTION
**wcFst** is Weir & Cockerham'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 **wcFst** uses equations 1,2,3,4.
# OPTIONS
```
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
```
# EXIT VALUES
**0**
: Success
**not 0**
: Failure
# SEE ALSO
[vcflib](./vcflib.md)(1)
# OTHER
## Source code
[wcFst.cpp](https://github.com/vcflib/vcflib/blob/master/src/wcFst.cpp)
# LICENSE
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
<!--
Created with ./scripts/bin2md.rb scripts/bin2md-template.erb
-->
|
