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% SMOOTHER(1) smoother (vcflib) | smoother (VCF transformation)
% Erik Garrison and vcflib contributors
# 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](./vcflib.md)(1)
# OTHER
## Source code
[smoother.cpp](https://github.com/vcflib/vcflib/blob/master/src/smoother.cpp)
# LICENSE
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
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