genotypeSummary

       Erik Garrison and vcflib contributors.

genotypeSummary (vcflib)                                                                      GENOTYPESUMMARY(1)

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

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       not0  Failure

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

genotypeSummary

              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

vcflib(1)

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