WCFST(1)

NAME

wcFst

SYNOPSIS

wcFst –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

wcFst is Weir & Cockerham’s Fst for two populations. Negative values are VALID, they are sites which can be treated as zero Fst. For more information see Evolution, Vol. 38 N. 6 Nov 1984. Specifically wcFst uses equations 1,2,3,4.

OPTIONS

    Output : 3 columns :
         1. seqid
         2. position
         3. target allele frequency
         4. background allele frequency
         5. **wcFst**
    required: t,target     -- argument: a zero based comma separated list of target individuals corrisponding to VCF columns
    required: b,background -- argument: a zero based comma separated list of background individuals corrisponding to VCF columns
    required: f,file       -- argument: proper formatted VCF
    required, y,type       -- argument: genotype likelihood format; genotype : GT,GL,PL,GP
    optional: r,region     -- argument: a tabix compliant genomic range: seqid or seqid:start-end
    optional: d,deltaaf    -- argument: skip sites where the difference in allele frequencies is less than deltaaf, default is zero
    Type: statistics

EXIT VALUES

0   Success

not 0
    Failure

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS
Erik Garrison and vcflib contributors.