Introduction

Accurate inference of genealogical relationships between pairs of individuals is paramount in association studies, forensics and evolutionary analyses of wildlife populations. Current methods for relationship inference consider only a small set of close relationships and have limited to no power to distinguish between relationships with the same number of meioses separating the individuals under consideration (e.g. aunt-niece versus niece-aunt or first cousins versus great aunt-niece).We present CARROT (ClAssification of Relationships with ROTations), a novel framework for relationship inference that leverages linkage information to differentiate between rotated relationships, that is, between relationships with the same number of common ancestors and the same number of meioses separating the individuals under consideration. We demonstrate that CARROT clearly outperforms existing methods on simulated data. We also applied CARROT on four populations from Phase III of the HapMap Project and detected previously unreported pairs of third- and fourth-degree relatives.Source code for CARROT is freely available at http://carrot.stanford.edu.sofiakp@stanford.edu.

Publications

  1. Reconstruction of genealogical relationships with applications to Phase III of HapMap.
    Cite this
    Kyriazopoulou-Panagiotopoulou S, Kashef Haghighi D, Aerni SJ, Sundquist A, Bercovici S, Batzoglou S, 2011-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Sofia Kyriazopoulou-Panagiotopoulou
    Developer

    Department of Computer Science, Biomedical Informatics Training Program

  2. Dorna Kashef Haghighi
    Developer

  3. Sarah J Aerni
    Developer

  4. Andreas Sundquist
    Developer

  5. Sivan Bercovici
    Developer

  6. Serafim Batzoglou
    Investigator

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Summary
AccessionBT001779
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted BySerafim Batzoglou