Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond.

ABSTRACT: Data on hundreds or thousands of single nucleotide polymorphisms (SNPs) provide detailed information about the relationships between individuals, but currently few tools can turn this information into a multigenerational pedigree. I present the r package sequoia, which assigns parents, clusters half-siblings sharing an unsampled parent and assigns grandparents to half-sibships. Assignments are made after consideration of the likelihoods of all possible first-, second- and third-degree relationships between the focal individuals, as well as the traditional alternative of being unrelated. This careful exploration of the local likelihood surface is implemented in a fast, heuristic hill-climbing algorithm. Distinction between the various categories of second-degree relatives is possible when l

SUBMITTER: Huisman J 

PROVIDER: S-EPMC6849609 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature