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Bioinformatics Advance Access published online on November 15, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm549
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GWAsimulator: A rapid whole genome simulation program

Chun Li 1,* and Mingyao Li 2

1Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; 2Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA

*To whom correspondence should be addressed. Dr. Chun Li, E-mail: chun.li{at}vanderbilt.edu


  Abstract

Summary: GWAsimulator implements a rapid moving-window algorithm to simulate genotype data for case-control or population samples from genomic SNP chips. For case-control data, the program generates cases and controls according to a user-specified multi-locus disease model, and can simulate specific regions if desired. The program uses phased genotype data as input and has the flexibility of simulating genotypes for different populations and different genomic SNP chips. When the HapMap phased data are used, the simulated data have similar local LD patterns as the HapMap data. As genome-wide association (GWA) studies become increasingly popular and new GWA data analysis methods are being developed, we anticipate that GWAsimulator will be an important tool for evaluating performance of new GWA analysis methods.

Availability: The C++ source code, executables for Linux, Windows, and MacOS, manual, example data sets and analysis program are available at http://biostat.mc.vanderbilt.edu/GWAsimulator.

Contact: chun.li{at}vanderbilt.edu

Associate Editor: Prof. Martin Bishop

Received on July 20, 2007; revised on October 10, 2007; accepted on October 29, 2007

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