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. 65 66<!-- 67 Created with ./scripts/bin2md.rb scripts/bin2md-template.erb 68--> 69