Provided by: libvcflib-tools_1.0.9+dfsg1-2_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.