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.TH "SMOOTHER" "1" "" "smoother (vcflib)" "smoother (VCF transformation)"
.hy
.SH NAME
.PP
\f[B]smoother\f[R]
.SH SYNOPSIS
.PP
\f[B]smoother\f[R] \[en]format pFst \[en]file GPA.output.txt
.SH DESCRIPTION
.PP
smoothes is a method for window smoothing many of the GPAT++ formats.
.SH OPTIONS
.IP
.nf
\f[C]
**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
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.
MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
.SH AUTHORS
Erik Garrison and vcflib contributors.
|
