pFst

       Erik Garrison and vcflib contributors.

pFst (vcflib)                                                                                            PFST(1)

pFst is a probabilistic approach for detecting differences in allele frequencies between two populations.

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

pFst

              **pFst** is a likelihood ratio test (LRT) quantifying allele frequency
              differences between populations.  The LRT by default uses the binomial
              distribution.  If Genotype likelihoods are provided it uses a modified
              binomial that weights each allele count by its certainty.  If type is
              set to 'PO' the LRT uses a beta distribution to fit the allele
              frequency spectrum of the target and background.  PO requires the AD
              and DP genotype fields and requires at least two pools for the target
              and background.  The p-value calculated in **pFst** is based on the
              chi-squared distribution with one degree of freedom.

              Output : 3 columns :
                   1. seqid
                   2. position
                   3. **pFst** probability

              required: t,target     -- argument: a zero based comma separated list of target individuals corresponding to VCF columns
              required: b,background -- argument: a zero based comma separated list of background individuals corresponding to VCF columns
              required: f,file       -- argument: a properly formatted VCF.
              required: y,type       -- argument: genotype likelihood format ; genotypes: GP, GL or PL; pooled: PO
              optional: d,deltaaf    -- argument: skip sites where the difference in allele frequencies is less than deltaaf, default is zero
              optional: r,region     -- argument: a tabix compliant genomic range : seqid or seqid:start-end
              optional: c,counts     -- switch  : use genotype counts rather than genotype likelihoods to estimate parameters, default false

              Type: statistics

vcflib(1)

pFst –target 0,1,2,3,4,5,6,7 –background 11,12,13,16,17,19,22 –file my.vcf –deltaaf 0.1 –type PL