NAME

       bp_composite_LD -i filename.prettybase.txt --sortbyld > outfile

SYNOPSIS

         bp_composite_LD -i filename.prettybase [-o out.LD] [-f prettybase/csv] [--sortbyld] [--noconvertindels]

   DESCRIPTION
       This a script which allows an easy way to calculate composite LD.

   OPTIONS
       -i or --in     filename

       -f or --format genotype format (prettybase or CSV)

       --sortbyld     To see data sorted by LD instead of just all the
                      site1/site2 pair LD values.

       -o or --out    output filename, otherwise will print to STDOUT

       --noconvert    (applicable for prettybase format file only)
                      if specified will NOT attempt to convert indel
                      states to 'I' and delete states ('-') to 'D'.

       -h or --help   see this documentation

   AUTHOR Jason Stajich, Matthew Hahn
       For more information contact:

       Matthew Hahn, <matthew.hahn-at-duke.edu> Jason Stajich <jason-at-bioperl-dot-org>