wcFst

       Erik Garrison and vcflib contributors.

wcFst (vcflib)                                                                                          WCFST(1)

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.

0      Success

       not0  Failure

       Copyright  2011-2024  (C)  Erik Garrison and vcflib contributors.  MIT licensed.  Copyright 2020-2024 (C)
       Pjotr Prins.

wcFst

              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

vcflib(1)

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