1% POPSTATS(1) popStats (vcflib) | popStats (VCF statistics)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**popStats**
7
8# SYNOPSIS
9
10popStat --type PL --target 0,1,2,3,4,5,6,7 --file my.vcf
11
12# DESCRIPTION
13
14General population genetic statistics for each SNP
15
16
17
18# OPTIONS
19
20```
21
22
23
24  Calculates basic population statistics at bi-allelic sites. The allele frequency is the number of non-reference alleles divided by the total number of alleles.  The expected hetrozygosity is 2*p*q, where p is the non-reference allele frequency and q is 1-p.  The observed heterozgosity is the fraction of 0/1 genotypes out of all genotypes.  The inbreeding coefficent, Fis, is the relative heterozygosity of each individual vs. compared to the target group.
25
26Output : 9 columns :
27     1. seqid
28     2. position
29     3. target allele frequency
30     4. expected heterozygosity
31     5. observed heterozygosity
32     6. number of hets
33     7. number of homozygous ref
34     8. number of homozygous alt
35     9. target Fis
36required: t,target     -- a zero based comma separated list of target individuals corresponding to VCF columns
37required: f,file       -- proper formatted VCF
38required, y,type       -- genotype likelihood format; genotype : GL,PL,GP
39optional, r,region     -- a tabix compliant region : chr1:1-1000 or chr1
40
41Type: statistics
42
43
44```
45
46
47
48
49
50# EXIT VALUES
51
52**0**
53: Success
54
55**not 0**
56: Failure
57
58# SEE ALSO
59
60
61
62[vcflib](./vcflib.md)(1)
63
64
65
66# OTHER
67
68## Source code
69
70[popStats.cpp](https://github.com/vcflib/vcflib/blob/master/src/popStats.cpp)
71
72# LICENSE
73
74Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
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