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Bioinformatics Advance Access originally published online on May 17, 2007
Bioinformatics 2007 23(14):1807-1814; doi:10.1093/bioinformatics/btm260
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations

Donna M. Toleno , Peter L. Morrell and Michael T. Clegg *

Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Errors in nucleotide sequence and SNP genotyping data are problematic when inferring haplotypes. Previously published methods for error detection in haplotype data make use of pedigree information; however, for many samples, individuals are not related by pedigree. This article describes a method for detecting errors in haplotypes by considering the recombinational history implied by the patterns of variation, three SNPs at a time.

Results: Coalescent simulations provide evidence that the method is robust to high levels of recombination as well as homologous gene conversion, indicating that patterns produced by both proximate and distant SNPs may be useful for detecting unlikely three-site haplotypes.

Availability: The perl script implementing the described method is called EDUT (Error Detection Using Triplets) and is available on request from the authors.

Contact: mclegg{at}uci.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on December 13, 2006; revised on April 30, 2007; accepted on May 9, 2007

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