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Bioinformatics Advance Access published online on April 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm138
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GENOME: a rapid coalescent-based whole genome simulator

Liming Liang *, Sebastian Zöllner and Gonçalo R. Abecasis

Center for Statistical Genetics, Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109, USA

*To whom correspondence should be addressed. Liming Liang, E-mail: lianglim{at}umich.edu


  Abstract

Summary: GENOME proposes a rapid coalescent-based approach to simulate whole genome data. In addition to features of standard coalescent simulators, the program allows for recombination rates to vary along the genome and for flexible population histories. Within small regions, we have evaluated samples simulated by GENOME to verify that GENOME provides the expected LD patterns and frequency spectra. The program can be used to study the sampling properties of any statistic for a whole genome study.

Availability: The program and C++ source code are available online at: http://www.sph.umich.edu/csg/liang/genome/

Associate Editor: Prof. Martin Bishop

Received on March 14, 2007; revised on March 14, 2007; accepted on April 3, 2007

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