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. 76 77<!-- 78 Created with ./scripts/bin2md.rb scripts/bin2md-template.erb 79--> 80