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

# pFst(1)

## NAME

**pFst**

## SYNOPSIS

**pFst** –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

**pFst** is a probabilistic approach for detecting differences in allele frequencies between two populations.

## OPTIONS

-

  ```
  **pFst** is a likelihood ratio test (LRT) quantifying allele frequency
  differences between populations.  The LRT by default uses the binomial
  distribution.  If Genotype likelihoods are provided it uses a modified
  binomial that weights each allele count by its certainty.  If type is
  set to 'PO' the LRT uses a beta distribution to fit the allele
  frequency spectrum of the target and background.  PO requires the AD
  and DP genotype fields and requires at least two pools for the target
  and background.  The p-value calculated in **pFst** is based on the
  chi-squared distribution with one degree of freedom.
  Output : 3 columns :
       1. seqid
       2. position
       3. **pFst** probability
  required: t,target     -- argument: a zero based comma separated list of target individuals corresponding to VCF columns
  required: b,background -- argument: a zero based comma separated list of background individuals corresponding to VCF columns
  required: f,file       -- argument: a properly formatted VCF.
  required: y,type       -- argument: genotype likelihood format ; genotypes: GP, GL or PL; pooled: PO
  optional: d,deltaaf    -- argument: skip sites where the difference in allele frequencies is less than deltaaf, default is zero
  optional: r,region     -- argument: a tabix compliant genomic range : seqid or seqid:start-end
  optional: c,counts     -- switch  : use genotype counts rather than genotype likelihoods to estimate parameters, default false
  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.