1% SMOOTHER(1) smoother (vcflib) | smoother (VCF transformation)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**smoother**
7
8# SYNOPSIS
9
10**smoother** --format pFst --file GPA.output.txt
11
12# DESCRIPTION
13
14smoothes is a method for window smoothing many of the GPAT++ formats.
15
16
17
18# OPTIONS
19
20```
21
22
23      **smoother** averages a set of scores over a sliding genomic window.
24      **smoother** slides over genomic positions not the SNP indices. In other words
25      the number of scores within a window will not be constant. The last
26      window for each seqid can be smaller than the defined window size.
27      **smoother** automatically analyses different seqids separately.
28Output : 4 columns :
29     1. seqid
30     2. window start
31     2. window end
32     3. averaged score
33
34required: f,file     -- argument: a file created by GPAT++
35required: o,format   -- argument: format of input file, case sensitive
36                              available format options:
37                                wcFst, pFst, bFst, iHS, xpEHH, abba-baba, col3
38optional: w,window   -- argument: size of genomic window in base pairs (default 5000)
39optional: s,step     -- argument: window step size in base pairs (default 1000)
40optional: t,truncate -- flag    : end last window at last position (zero based)
41
42Type: transformation
43
44
45```
46
47
48
49
50
51# EXIT VALUES
52
53**0**
54: Success
55
56**not 0**
57: Failure
58
59# SEE ALSO
60
61
62
63[vcflib](./vcflib.md)(1)
64
65
66
67# OTHER
68
69## Source code
70
71[smoother.cpp](https://github.com/vcflib/vcflib/blob/master/src/smoother.cpp)
72
73# LICENSE
74
75Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
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