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PFST(1) pFst (VCF statistics) PFST(1) NAME pFst SYNOPSIS pFst -target 0,1,2,3,4,5,6,7 -background 11,12,13,16,17,19,22 -file my.vcf -deltaaf 0.1 -type PL DESCRIPTION pFst is a probabilistic approach for detecting differences in allele frequencies between two populations. OPTIONS **pFst** is a likelihood ratio test (LRT) quantifying allele frequency differences between populations. The LRT by default uses the binomial distribution. If Genotype likelihoods are provided it uses a modified binomial that weights each allele count by its certainty. If type is set to 'PO' the LRT uses a beta distribution to fit the allele frequency spectrum of the target and background. PO requires the AD and DP genotype fields and requires at least two pools for the target and background. The p-value calculated in **pFst** is based on the chi-squared distribution with one degree of freedom. Output : 3 columns : 1. seqid 2. position 3. **pFst** probability required: t,target -- argument: a zero based comma separated list of target individuals corresponding to VCF columns required: b,background -- argument: a zero based comma separated list of background individuals corresponding to VCF columns required: f,file -- argument: a properly formatted VCF. required: y,type -- argument: genotype likelihood format ; genotypes: GP, GL or PL; pooled: PO optional: d,deltaaf -- argument: skip sites where the difference in allele frequencies is less than deltaaf, default is zero optional: r,region -- argument: a tabix compliant genomic range : seqid or seqid:start-end optional: c,counts -- switch : use genotype counts rather than genotype likelihoods to estimate parameters, default false 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. pFst (vcflib) PFST(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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