WCFST

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

AUTHORS

Erik Garrison and vcflib contributors.