Provided by: libvcflib-tools_1.0.3+dfsg-1_amd64 bug

NAME
       bFst


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


DESCRIPTION
       bFst is a Bayesian approach to Fst.  Importantly bFst accounts for genotype uncertainty in
       the model using genotype likelihoods.  For a more detailed description  see:  `A  Bayesian
       approach  to  inferring  population  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  index,
       within  each subpopulation), a free parameter for the total population’s allele frequency,
       and Fst.


OPTIONS
              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


EXIT VALUES
       0      Success

       not 0  Failure


SEE ALSO
       vcflib(1)


OTHER
LICENSE
       Copyright 2011-2022 (C) Erik Garrison and vcflib contributors.  MIT licensed.


AUTHORS
       Erik Garrison and vcflib contributors.