1% SEQUENCEDIVERSITY(1) sequenceDiversity (vcflib) | sequenceDiversity (VCF statistics)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**sequenceDiversity**
7
8# SYNOPSIS
9
10**sequenceDiversity** --target 0,1,2,3,4,5,6,7 --file my.vcf
11
12# DESCRIPTION
13
14The **sequenceDiversity** program calculates two popular metrics of haplotype diversity: pi and extended haplotype homozygoisty (eHH). Pi is calculated using the Nei and Li 1979 formulation. eHH a convenient way to think about haplotype diversity. When eHH = 0 all haplotypes in the window are unique and when eHH = 1 all haplotypes in the window are identical.
15
16
17
18# OPTIONS
19
20```
21
22
23Output : 5 columns:
24         1.  seqid
25         2.  start of window
26         3.  end of window
27         4.  pi
28         5.  eHH
29
30
31required: t,target     -- argument: a zero base comma separated list of target individuals corresponding to VCF columns
32required: f,file       -- argument: a properly formatted phased VCF file
33required: y,type       -- argument: type of genotype likelihood: PL, GL or GP
34optional: a,af         -- sites less than af  are filtered out; default is 0
35optional: r,region     -- argument: a tabix compliant region : "seqid:0-100" or "seqid"
36optional: w,window     -- argument: the number of SNPs per window; default is 20
37
38Type: statistics
39
40
41
42```
43
44
45
46
47
48# EXIT VALUES
49
50**0**
51: Success
52
53**not 0**
54: Failure
55
56# SEE ALSO
57
58
59
60[vcflib](./vcflib.md)(1)
61
62
63
64# OTHER
65
66## Source code
67
68[sequenceDiversity.cpp](https://github.com/vcflib/vcflib/blob/master/src/sequenceDiversity.cpp)
69
70# LICENSE
71
72Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
73
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