popStats

       Erik Garrison and vcflib contributors.

popStats (vcflib)                                                                                    POPSTATS(1)

       General population genetic statistics for each SNP

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       Copyright  2011-2024  (C)  Erik Garrison and vcflib contributors.  MIT licensed.  Copyright 2020-2024 (C)
       Pjotr Prins.

popStats

                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

vcflib(1)

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