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.\" Automatically generated by Pandoc 2.7.3
.\"
.TH "GENOTYPESUMMARY" "1" "" "genotypeSummary (vcflib)" "genotypeSummary (VCF
statistics)"
.hy
.SH NAME
.PP
\f[B]genotypeSummary\f[R]
.SH SYNOPSIS
.PP
genotypeSummmary \[en]type PL \[en]target 0,1,2,3,4,5,6,7 \[en]file
my.vcf \[en]snp
.SH DESCRIPTION
.PP
Generates a table of genotype counts.
Summarizes genotype counts for bi-allelic SNVs and indel
.SH OPTIONS
.IP
.nf
\f[C]
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
\f[R]
.fi
.SH EXIT VALUES
.TP
.B \f[B]0\f[R]
Success
.TP
.B \f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2020 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.
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