Smoothing with GPAT - zeeev/vcflib GitHub Wiki

usage for the smoother program :

INFO: help
INFO: description:
      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 seperately.
Output : 4 columns :
     1. seqid
     2. window start
     2. window end
     3. averaged score

INFO: usage: smoother --format pFst --file GPA.output.txt

INFO: required: f,file     -- argument: a file created by GPAT++
INFO: required: o,format   -- argument: format of input file, case sensative
                              availible format options:
                                wcFst, pFst, bFst, iHS, xpEHH, abba-baba
INFO: optional: w,window   -- argument: size of genomic window in base pairs (default 5000)
INFO: optional: s,step     -- argument: window step size in base pairs (default 1000)

INFO: version 1.0.0 ; date: April 2014 ; author: Zev Kronenberg; email : [email protected]

Example with provided data:

../bin/smoother --file 612.nocounts -w 1000 -s 100 -o pFst > 612.nocounts.smoothed
R --vanilla < ../bin/plotSmoothed.R --args 612.nocounts.smoothed pFst

The resulting output: