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

# permuteSmooth(1)

## NAME

**permuteSmooth**

## SYNOPSIS

**permuteSmooth** -s wcFst.smooth.txt -f wcFst.txt -n 5 -s 1

## DESCRIPTION

**permuteSmooth** is a method for adding empirical p-values smoothed wcFst scores.

## OPTIONS

-

  ```
  Required:
        file:     f   -- argument: original wcFst data
        smoothed: s   -- argument: smoothed wcFst data
        format:   y   -- argument: [swcFst, segwcFst]
  Optional:
        number:   n   -- argument: the number of permutations to run for each value [1000]
        success:  u   -- argument: stop permutations after 's' successes [1]
        success:  x   -- argument: number of threads [1]
  OUTPUT: **permuteSmooth** will append three additional columns:
          1. The number of successes
          2. The number of trials
          3. The empirical p-value
  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.