genotypeSummary.md

% GENOTYPESUMMARY(1) genotypeSummary (vcflib) | genotypeSummary (VCF statistics) % Erik Garrison and vcflib contributors

NAME

genotypeSummary

SYNOPSIS

genotypeSummmary --type PL --target 0,1,2,3,4,5,6,7 --file my.vcf --snp

DESCRIPTION

Generates a table of genotype counts. Summarizes genotype counts for bi-allelic SNVs and indel

OPTIONS

output: table of genotype counts for each individual.
required: t,target     -- a zero based comma separated list of target individuals corresponding to VCF columns        
required: f,file       -- proper formatted VCF                                                                        
required, y,type       -- genotype likelihood format; genotype : GL,PL,GP                                             
optional, r,region     -- a tabix compliant region : chr1:1-1000 or chr1                                              
optional, s,snp        -- Only count SNPs                                              
optional, a,ancestral  -- describe counts relative to the ancestral allele defined as AA in INFO

Type: statistics

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

genotypeSummary.cpp

LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.