smoother.md

% SMOOTHER(1) smoother (vcflib) | smoother (VCF transformation) % Erik Garrison and vcflib contributors

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

Source code

smoother.cpp

LICENSE

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.