1% PVST(1) pVst (vcflib) | pVst (VCF statistics)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**pVst**
7
8# SYNOPSIS
9
10**pVst** --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf --type CN
11
12# DESCRIPTION
13
14**pVst** calculates vst, a measure of CNV stratification.
15
16
17
18# OPTIONS
19
20```
21
22
23
24
25The statistic Vst is used to test the difference in copy numbers at
26each SV between two groups: Vst = (Vt-Vs)/Vt, where Vt is the overall
27variance of copy number and Vs the average variance within
28populations.
29
30Output : 4 columns :
31     1. seqid
32     2. position
33     3. end
34     3. vst
35     4. probability
36
37required: t,target     -- argument: a zero based comma separated list of target individuals corresponding to VCF columns
38required: b,background -- argument: a zero based comma separated list of background individuals corresponding to VCF columns
39required: f,file       -- argument: a properly formatted VCF.
40required: y,type       -- argument: the genotype field with the copy number: e.g. CN|CNF
41optional: r,region     -- argument: a tabix compliant genomic range : seqid or seqid:start-end
42optional: x,cpu        -- argument: number of CPUs [1]
43optional: n,per        -- argument: number of permutations [1000]
44
45Type: statistics
46
47
48
49```
50
51
52
53
54
55# EXIT VALUES
56
57**0**
58: Success
59
60**not 0**
61: Failure
62
63# SEE ALSO
64
65
66
67[vcflib](./vcflib.md)(1)
68
69
70
71# OTHER
72
73## Source code
74
75[pVst.cpp](https://github.com/vcflib/vcflib/blob/master/src/pVst.cpp)
76
77# LICENSE
78
79Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
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