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


BACKGROUND
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
Hao
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K
Algorithm and Data Analysis, Affymetrix Inc. 3420 Central Expressway, Santa Clara, California, USA. ke_hao@affymetrix.com
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Cawley
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D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D015810:Linkage Disequilibrium / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013223:Statistics as Topic
D005819:Genetic Markers