Christopher Fields
and 4 contributors


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


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


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


-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, <> Jason Stajich <jason-at-bioperl-dot-org>