---
name: "wcFst"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/wcFst"
---

# 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)](/vcflib/1.md)

## 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.