Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with n individuals genotyped at every site, a set of Mendelian-consistent haplotypes that have the minimum number of recombinations. This is an NP-hard problem and some pedigrees can have thousands of individuals and hundreds of thousands of sites. This paper formulates this problem as a optimization on a graph and introduces a tailored algorithm with a running time of O(n(k+2)m6k) for n individuals, m sites, and k recombinations. Since there are generally only 1-2 recombinations per chromosome in each meiosis, k is small enough to make this algorithm practically relevant.
CITATION STYLE
Kirkpatrick, B. (2016). Haplotype inference for pedigrees with few recombinations. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 9683, pp. 269–283). Springer Verlag. https://doi.org/10.1007/978-3-319-38782-6_23
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