1% GENOTYPESUMMARY(1) genotypeSummary (vcflib) | genotypeSummary (VCF statistics)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**genotypeSummary**
7
8# SYNOPSIS
9
10genotypeSummmary --type PL --target 0,1,2,3,4,5,6,7 --file my.vcf --snp
11
12# DESCRIPTION
13
14Generates a table of genotype counts. Summarizes genotype counts for bi-allelic SNVs and indel
15
16
17
18# OPTIONS
19
20```
21
22
23output: table of genotype counts for each individual.
24required: t,target     -- a zero based comma separated list of target individuals corresponding to VCF columns
25required: f,file       -- proper formatted VCF
26required, y,type       -- genotype likelihood format; genotype : GL,PL,GP
27optional, r,region     -- a tabix compliant region : chr1:1-1000 or chr1
28optional, s,snp        -- Only count SNPs
29optional, a,ancestral  -- describe counts relative to the ancestral allele defined as AA in INFO
30
31Type: statistics
32
33
34```
35
36
37
38
39
40# EXIT VALUES
41
42**0**
43: Success
44
45**not 0**
46: Failure
47
48# SEE ALSO
49
50
51
52[vcflib](./vcflib.md)(1)
53
54
55
56# OTHER
57
58## Source code
59
60[genotypeSummary.cpp](https://github.com/vcflib/vcflib/blob/master/src/genotypeSummary.cpp)
61
62# LICENSE
63
64Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
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