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 2011-2023 (C) Erik Garrison and vcflib contributors.  MIT licensed.

AUTHORS

       Erik Garrison and vcflib contributors.