Man page - wcfst(1)
Packages contas this manual
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- vcfprimers(1)
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- vcf2fasta(1)
- vcfglxgt(1)
- vcffixup(1)
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- vcfcat(1)
- vcfintersect(1)
- vcfflatten(1)
- vcfaltcount(1)
- vcfkeepsamples(1)
- vcfdistance(1)
- vcfaddinfo(1)
- vcfgeno2alleles(1)
- vcfrandomsample(1)
- vcfhetcount(1)
- vcfafpath(1)
- vcfroc(1)
Package: libvcflib-tools
apt-get install libvcflib-tools
apt-get install libvcflib-tools
Manuals in package:
Documentations in package:
Manual
| WCFST(1) | wcFst (VCF statistics) | 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 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.
AUTHORS
Erik Garrison and vcflib contributors.
| wcFst (vcflib) |