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)

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.