% GENOTYPESUMMARY(1) genotypeSummary (vcflib) | genotypeSummary (VCF statistics) % Erik Garrison and vcflib contributors
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
0 : Success
not 0 : Failure
vcflib(1)
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.