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. 2014 Aug 7;10(8):e1004528. doi: 10.1371/journal.pgen.1004528

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© 2014 Mathieson, McVean

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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A: Algorithm for detecting haplotypes. For each variant in the sample (green), we scan left and right until we find inconsistent homozygote genotypes (red), record the physical and genetic length of this region (blue), and the number of singletons (purple). B: Model for haplotype age . Consider the 4 chromosomes (grey) of the two individuals sharing an haplotype (blue). We model the total genetic length of the inferred haplotype, , as the sum of the true genetic length and an error . Similarly, we model the number of singletons as the sum of the number on the shared chromosome () and the number on the unshared chromosomes, . We ignore the fact that we overestimate and therefore that some of the singletons might lie in the unshared part of the chromosome.

Inline graphic — A: Algorithm for detecting haplotypes. For each variant in the sample (green), we scan left and right until we find inconsistent homozygote genotypes (red), record the physical and genetic length of this region (blue), and the number of singletons (purple). B: Model for haplotype age . Consider the 4 chromosomes (grey) of the two individuals sharing an haplotype (blue). We model the total genetic length of the inferred haplotype, , as the sum of the true genetic length and an error . Similarly, we model the number of singletons as the sum of the number on the shared chromosome () and the number on the unshared chromosomes, . We ignore the fact that we overestimate and therefore that some of the singletons might lie in the unshared part of the chromosome.