Man page - bfst(1)

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libvcflib-tools

Manual

BFST

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS

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

OTHER

LICENSE

AUTHORS

Erik Garrison and vcflib contributors.