License: -------- 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.