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

NAME

SYNOPSIS

DESCRIPTION

OPTIONS

EXIT VALUES

SEE ALSO

OTHER

LICENSE

AUTHORS