DOKK / manpages / debian 12 / libvcflib-tools / genotypeSummary.1.en
GENOTYPESUMMARY(1) genotypeSummary (VCF statistics) GENOTYPESUMMARY(1)

genotypeSummary

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

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

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

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vcflib(1)

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

Erik Garrison and vcflib contributors.

genotypeSummary (vcflib)