NAME

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

SYNOPSIS

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 Bio::Seq

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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