BFST(1) bFst (VCF statistics) BFST(1) 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 likeli- hoods provided by variant callers. There are five free parameters esti- mated in the model: each subpopulation's allele frequency and Fis (fixation index, within each subpopulation), a free parameter for the total popula- tion'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 2011-2025 (C) Erik Garrison and vcflib contributors. MIT li- censed. Copyright 2020-2025 (C) Pjotr Prins. AUTHORS Erik Garrison and vcflib contributors. bFst (vcflib) BFST(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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