WCFST(1) wcFst (VCF statistics) WCFST(1)

wcFst

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

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.

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

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vcflib(1)

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

Erik Garrison and vcflib contributors.

wcFst (vcflib)