IPEDIPED 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). DownloadManualTo 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:
News
PublicationDan 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. ContactFor general questions, comments, suggestions, bug report about IPED, please email Dan He (hedanus (AT) gmail.com, dhe (AT) us.ibm.com). |