ibdadmx.py
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.
https://github.com/itamareskin/IBDAdmixed
ibadmx.py is a python program for detecting segments of identity-by-descent (IBD) on datasets of admixed individuals. The program was developed by Itamar (Eskin) Afek at Tel Aviv University. Full description of the algorithm is included in the paper "IBDAdmixed: Fine-Scale Detection of Identity-by-Descent in Admixed Populations".
Python 2.6
Cython
After downloading the source code, navigate to the lib subdirectory and run the following in a unix command line:
python setup.py build_ext --inplace
For detailed usage instruction, run:
python ibadmx.py --help
input prefix of input files (.dat,.map in IBDAdmixed/LAMP format)
out output prefix
hapmodelfile .dag beagle model file name (one for each ancestry)
-h, --help show this help message and exit
-k K, --num-anc K set number of ancestries
-a ALPHAS [ALPHAS ...], --set-alphas ALPHAS [ALPHAS ...] set the alphas
-g GENERATIONS, --generations GENERATIONS set the number of generations of admixture
-n NUM_SNPS, --max-snps NUM_SNPS maximal number of snps to be used
-p NUM_CPUS, --num-cpus NUM_CPUS number of cpus to be used
-e EPSILON, --epsilon EPSILON epsilon for error
-m MIN_SCORE, --min-score MIN_SCORE minimal score to report as IBD
-w WIN_SIZE, --win-size WIN_SIZE window size (in number of SNPs)
-o OFFSET, --offset OFFSET offset for windows (in number of SNPs)
--pair PAIR PAIR single pair to process
--pairs-file PAIRS_FILE file containing pairs of individuals to process
--germline-file GERMLINEFILE germline results file
--set-ibd-trans IBD_TRANS [IBD_TRANS ...] set ibd to no IBD probabilities
--debug print debugging information
--phased use phased mode
--naive-model use naive model
--scramble scramble phase of genotypes
--condor send jobs to htcondor
--keep-temp keep temoporary files
--rerun rerun failed jobs
--recover recover results from all finished jobs
In a unix command line, run: python -m unittest discover