Provided by: libvcflib-tools_1.0.9+dfsg1-3build1_amd64 bug

NAME

       popStats

SYNOPSIS

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

DESCRIPTION

       General population genetic statistics for each SNP

OPTIONS

                Calculates basic population statistics at bi-allelic sites. The allele frequency is the number of non-reference alleles divided by the total number of alleles.  The expected hetrozygosity is 2*p*q, where p is the non-reference allele frequency and q is 1-p.  The observed heterozgosity is the fraction of 0/1 genotypes out of all genotypes.  The inbreeding coefficient, Fis, is the relative heterozygosity of each individual vs. compared to the target group.

              Output : 9 columns :
                   1. seqid
                   2. position
                   3. target allele frequency
                   4. expected heterozygosity
                   5. observed heterozygosity
                   6. number of hets
                   7. number of homozygous ref
                   8. number of homozygous alt
                   9. target Fis
              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

              Type: statistics

EXIT VALUES

       0      Success

       not 0  Failure

SEE ALSO

       vcflib(1)

OTHER

LICENSE

       Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.  MIT licensed.

AUTHORS

       Erik Garrison and vcflib contributors.