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

# smoother(1)

## NAME

**smoother**

## SYNOPSIS

**smoother** –format pFst –file GPA.output.txt

## DESCRIPTION

smoothes is a method for window smoothing many of the GPAT++ formats.

## OPTIONS

-

  ```
        **smoother** averages a set of scores over a sliding genomic window.
        **smoother** slides over genomic positions not the SNP indices. In other words
        the number of scores within a window will not be constant. The last
        window for each seqid can be smaller than the defined window size.
        **smoother** automatically analyses different seqids separately.
  Output : 4 columns :
       1. seqid
       2. window start
       2. window end
       3. averaged score
  required: f,file     -- argument: a file created by GPAT++
  required: o,format   -- argument: format of input file, case sensitive
                                available format options:
                                  wcFst, pFst, bFst, iHS, xpEHH, abba-baba, col3
  optional: w,window   -- argument: size of genomic window in base pairs (default 5000)
  optional: s,step     -- argument: window step size in base pairs (default 1000)
  optional: t,truncate -- flag    : end last window at last position (zero based)
  Type: transformation
  ```

## 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.