bFst

       Erik Garrison and vcflib contributors.

bFst (vcflib)                                                                                            BFST(1)

bFst  is a Bayesian approach to Fst.  Importantly bFst accounts for genotype uncertainty in the model us‐
       ing genotype likelihoods.  For a more detailed description see: `A Bayesian approach to inferring popula‐
       tion structure from dominant markers’ by Holsinger et al. Molecular Ecology Vol 11, issue  7  2002.   The
       likelihood function has been modified to use genotype likelihoods provided by variant callers.  There are
       five  free parameters estimated in the model: each subpopulation’s allele frequency and Fis (fixation in‐
       dex, within each subpopulation), a free parameter for the total population’s allele frequency, and Fst.

0      Success

       not0  Failure

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

bFst

              Output : 11 columns :
                   1.  Seqid
                   2.  Position
                   3.  Observed allele frequency in target.
                   4.  Estimated allele frequency in target.
                   5.  Observed allele frequency in background.
                   6.  Estimated allele frequency in background.
                   7.  Observed allele frequency combined.
                   8.  Estimated allele frequency in combined.
                   9.  ML estimate of Fst (mean)
                   10. Lower bound of the 95% credible interval
                   11. Upper bound of the 95% credible interval

              required: t,target     -- a zero bases comma separated list of target individuals corrisponding to VCF columns
              required: b,background -- a zero bases comma separated list of background individuals corrisponding to VCF columns
              required: f,file a     -- a proper formatted VCF file.  the FORMAT field MUST contain "PL"
              required: d,deltaaf    -- skip sites were the difference in allele frequency is less than deltaaf

              Type: statistics

vcflib(1)

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