GENOTYPESUMMARY

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

LICENSE

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

AUTHORS

Erik Garrison and vcflib contributors.