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

# permuteGPAT++(1)

## NAME

**permuteGPAT++**

## SYNOPSIS

**permuteGPAT++** -f gpat.txt -n 5 -s 1

## DESCRIPTION

**permuteGPAT++** is a method for adding empirical p-values to a GPAT++ score.

## OPTIONS

-

  ```
       Currently **permuteGPAT++** only supports wcFst, but will be extended.
  OUTPUT: **permuteGPAT++** will append three additional columns:
          1. The number of successes
          2. The number of trials
          3. The empirical p-value
  file:    f   -- argument: the input file
  number:  n   -- argument: the number of permutations to run for each value [1000]
  success: s   -- argument: stop permutations after 's' successes [1]
  Type: phenotype
  ```

## 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.