IPED

IPED is a method to reconstruct pedigree from genotype data.

IPED was created byy Dan He

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

Download

Download IPED

Manual

To run IPED, from the command line:

java -jar IPED.jar -i [num_of_extant_individuals] -d [num_of_generations] -f [ibd_file]

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

-d: num_of_generations: the number of generations you want to reconstruct

-f: ibd_file: the input ibd file for the extant individuals. One row for each haplotype of each extant individual. Row 1 and 2 are the two haplotypes for the first individual. Row 3 and 4 are the two haplotypes of the second individual and so on. The haplotypes are divided into chunks at the same positions. Therefore each row is a set of haplotype chunks. Each chunk is assigned an index. Two haplotypes are IBD at the same chunk if they share the same index. In the following example:

1 3 4 9
2 3 4 8


There are two haplotypes, one for each row. Each haplotypes have 4 chunks. They are IBD at the second and third chunks. A pedigree simulator adapted by Zhanyong Wang from the simulator of Bonnie Kirkpatrick is included to generate such ibd files.

output: The reconstructed pedigree. The output file is: pedigree.out. The index of the extant individuals are consistent with the index of the individuals in the ibd_file.

News

  • v1.1 (2013-10-14) version 1.1 was released.

Publication

Dan He, Z Wang, B Han, L Parida, E Eskin: IPED: Inheritance path based pedigree reconstruction algorithm using genotype data, Research in Computational Molecular Biology (Recomb 2013), Beijing, China, April 7 - 10, 2013, also in Journal of Computational Biology, (2013). Read more.

Please cite the above paper if you are using the IPED Software.

Contact

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