Rapidly registering identity-by-descent across ancestral recombination graphs

Shuo Yang, Shai Carmi, Itsik Pe’er

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


The genomes of remotely related individuals occasionally contain long segments that are Identical By Descent (IBD). Sharing of IBD segments has many applications in population and medical genetics, and it is thus desirable to study their properties in simulations. However, no current method provides a direct, efficient means to extract IBD segments from simulated genealogies. Here, we introduce computationally efficient approaches to extract ground-truth IBD segments from a sequence of genealogies, or equivalently, an ancestral recombination graph. Specifically, we use a two-step scheme, where we first identify putative shared segments by comparing the common ancestors of all pairs of individuals at some distance apart. This reduces the search space considerably, and we then proceed by determining the true IBD status of the candidate segments. Under some assumptions and when allowing a limited resolution of segment lengths, our run-time complexity is reduced from O(n3 log n) for the naïve algorithm to O(n log n), where n is the number of individuals in the sample.

Original languageAmerican English
Title of host publicationResearch in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings
EditorsTeresa M. Przytycka
PublisherSpringer Verlag
Number of pages14
ISBN (Electronic)9783319167053
StatePublished - 2015
Externally publishedYes
Event19th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2015 - Warsaw, Poland
Duration: 12 Apr 201515 Apr 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference19th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2015

Bibliographical note

Publisher Copyright:
© Springer International Publishing Switzerland 2015.


  • Ancestral Recombination Graphs
  • Identity by Descent
  • Population Genetics
  • Simulation


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