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
For more information contact:
Matthew Hahn, <matthew.hahn-at-duke.edu> Jason Stajich <jason-at-bioperl-dot-org>
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.