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.TH "BFST" "1" "" "bFst (vcflib)" "bFst (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]bFst\f[R]
.SH SYNOPSIS
.PP
\f[B]bFst\f[R] \[en]target 0,1,2,3,4,5,6,7 \[en]background
11,12,13,16,17,19,22 \[en]file my.vcf \[en]deltaaf 0.1
.SH DESCRIPTION
.PP
\f[B]bFst\f[R] is a Bayesian approach to Fst.
Importantly \f[B]bFst\f[R] accounts for genotype uncertainty in the
model using genotype likelihoods.
For a more detailed description see: \[ga]A Bayesian approach to
inferring population structure from dominant markers\[cq] 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\[cq]s allele frequency and Fis (fixation index, within
each subpopulation), a free parameter for the total population\[cq]s
allele frequency, and Fst.
.SH OPTIONS
.IP
.nf
\f[C]

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 \[dq]PL\[dq]
required: d,deltaaf    -- skip sites were the difference in allele frequency is less than deltaaf


Type: statistics
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.