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Bioinformatics Advance Access published online on December 5, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl574
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© 2006 The Author(s)
Received August 17, 2006
Revised November 10, 2006
Accepted November 12, 2006

Applications note

LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage

K. Hao 1 * {dagger}, X. Di 1 {dagger}, and S. Cawley 1 {dagger}

1 Algorithm and Data Analysis, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California

* To whom correspondence should be addressed.
K. Hao, E-mail: ke_hao{at}affymetrix.com


  Abstract

Summary: The scale of genetic-variation data sets has increased enormously and the linkage equilibrium (LD) structure of these polymorphisms, particularly in whole-genome association studies, is of great interest. The significant computational complexity of calculating single- and multiple-marker correlations at a genome-wide scale remains challenging. We have developed a program that efficiently characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations.

Availability: LdCompare is licensed under the GNU General Public License (GPL). Source code, documentation, testing datasets, and precompiled executables are available for download at: http://www.affymetrix.com/support/developer/tools/devnettools.affx.

Associate Editor: Martin Bishop

{dagger}Equal authors


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