IBD-Groupon

IBD-Groupon is a method to detect group-wise IBD tracts based on pairwise IBD relationships

IBD-Groupon was created by Dan He

For general questions, comments or suggestions about IBD-Groupon, please email Dan He (danhe (AT) cs.ucla.edu, dhe (AT) us.ibm.com).

Download

Download IBD-Groupon

Manual

To run IBD-Groupon, from the command line:

java -jar IBDGroupon.jar -i num_of_individuals -f pairwise_ibd_file -c chunk_file

-i: num_of_individuals: the number of individuals your data set has.

-f: pairwise_ibd_file: the input pairwise ibd file, which should be the output ibd file from Beagle. The index of the two haplotypes of the same individual should be individual_index_1, individual_index _2, respectively.

-c: chunk_file: the maximum IBD chunks. You need to identify the chunks according to the pairwise_ibd_file yourself.

output: the group-wise IBD tracts for each chunk. Notice we consider the IBD tracts among the haplotypes instead of indivdiuals.

News

  • v1.1 (2013-09-29) version 1.1 was released.

  • v1.4 (2014-01-02) version 1.2 was released. Fixed a bug on setting the number of individuals from input.

Publication

Dan He: IBD-Groupon: An Efficient Method for Detecting Group-wise Identity-by-Descent regions simultaneously in Multiple Individuals based on Pairwise IBD relationships, The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2013), Berlin, Germany, July 21 - 23, 2013, also in Bioinformatics, 29(13), 162-170 (2013). Read more.

Please cite the above paper if you are using the IBD-Groupon Software.

Contact

For general questions, comments, suggestions, bug report about IBD-Groupon, please email Dan He (hedanus (AT) gmail.com, dhe (AT) us.ibm.com).