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Bioinformatics Advance Access originally published online on December 5, 2006
Bioinformatics 2007 23(2):252-254; doi:10.1093/bioinformatics/btl574
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

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

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

*To whom correspondence should be addressed.


  Abstract

Summary: The scale of genetic-variation datasets 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

Contact: ke_hao{at}affymetrix.com

{dagger}The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors

Associate Editor: Martin Bishop

Received on September 21, 2006; revised on November 10, 2006; accepted on November 11, 2006

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