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License:
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haploscore.py haplotypes.py ibd.py threshold.py
Copyright (C) 2014 23andMe, Inc.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

If you have questions, please contact 23andMe, Inc. at
1390 Shorebird Way, Mountain View, CA 94043.

Program available for download at: 
----------------------------------
https://github.com/23andMe/ibd


About:
------
haploscore.py is a standalone program for computing HaploScore, a haplotype-based
metric that enables accurate IBD detection on population-scale datasets. It is
designed to post-process IBD segments obtained by GERMLINE
(http://www1.cs.columbia.edu/~gusev/germline/). The program was developed by
Eric Y. Durand and Cory Y. McLean at 23andMe, Inc. 

Usage:
------
For detailed usage instruction, run
python haploscore.py --help

Note that haplotype.py requires Python 2.7 and numpy 1.7.

Required Input:
---------------
match        GERMLINE-formatted match file. The format is described at http://www1.cs.columbia.edu/~gusev/germline/
ped_file     PLINK PED file containing the haplotypes used as input by GERMLINE
map_file     PLINK MAP file containing the physical map for the markers included in the PED file.

Options:
--------
--genotype_error VALUE  Set the genotyping error rate per marker to VALUE
--switch_error VALUE    Set the switch error rate per marker to VALUE
--filter VALUE          Set the mean overlap threshold desired to VALUE
--threshold_file FILE   Use the specified mean overlap threshold file FILE
-v, --verbose           Report progress to stderr
-h, --help              Print help message

Output:
-------
out_file  Output file. It is formatted like the match.gz file but contains an additional last column, the HaploScore value.
          If the --filter flag is specified, input segments not satisfying the HaploScore threshold criterion will be
          omitted from the output.

Testing:
--------
The test/ directory contains PLINK data as well as the expected GERMLINE results. 
The following command

  python haploscore.py test/expected.match test/CEU.22.ped test/CEU.22.map test/myoutfile

should produce test/myoutfile, identical to test/expected.match.scored. Similarly,

  python haploscore.py test/expected.match test/CEU.22.mixed.ped test/CEU.22.mixed.map test/myoutfile2

should produce test/myoutfile2, also identical to test/expected.match.scored.