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. 2015 Feb 25;4:7. doi: 10.1186/s13742-015-0047-8

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© Chang et al.; licensee BioMed Central. 2015

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Rapid classification of “recombination” variant pairs. This is a plot of 101 equally spaced D’ log-likelihoods for (rs58108140, rs140337953) in 1000 Genomes phase 1, used in Gabriel et al.’s method of identifying haplotype blocks. Whenever the upper end of the 90% confidence interval is smaller than 0.90 (i.e. the rightmost 11 likelihoods sum to less than 5% of the total), we have strong evidence for historical recombination between the two variants. After determining that L(D^′=x) has only one extreme value in [0, 1] and that it’s between 0.39 and 0.40, confirming L(D^′=0.90)<L(D^′=0.40)/220 is enough to finish classifying the variant pair (due to monotonicity: L(D^′=0.90)≥L(D^′=0.91)≥…≥L(D^′=1.00)); evaluation of the other 99 likelihoods is now skipped in this case. The dotted horizontal line is at L(D^′=0.40)/220.