Man page - wcfst(1)

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Manual

WCFST

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS

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

OTHER

LICENSE

AUTHORS

Erik Garrison and vcflib contributors.