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.
Bibliographical noteFunding Information:
The authors thank M. Brandt, C. Torres, L. DeRose, S. MacDonald and two anonymous reviewers for helpful comments on previous versions of the manuscript. This work was supported by National Science Foundation grant DEB-0129247.