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

BP_COMPOSITE_LD(1p) User Contributed Perl Documentation BP_COMPOSITE_LD(1p)

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>
2017-08-30 perl v5.26.0