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

AUTHORS
Erik Garrison and vcflib contributors.