1 Background
1.1 The core of Sequoia
- Assign genotyped parents to genotyped individuals (‘parentage assignment’), even if the sex or birth year of some candidate parents is unknown;
- Cluster genotyped half- and full-siblings for which the parent is not genotyped into sibships, assigning a ‘dummy parent’ to each sibship
- Find grandparents to each sibship, both among genotyped individuals and among dummy parents to other sibships.
Sequoia provides a conservative hill-climbing algorithm to construct a high-likelihood pedigree from data on hundreds of single nucleotide polymorphisms (SNPs), described in Huisman (2017). Explicit consideration of the likelihoods of alternative relationships (parent-offspring, full siblings, grandparent–grand-offspring, …) before making an assignment reduces the number of false positives, compared to parentage assignment methods that rely on the likelihood ratio between parent-offspring versus unrelated only (Thompson and Meagher 1987). The heuristic, sequential approach used is considerably quicker than most alternative approaches such as MCMC, and when genetic information is abundant there is little to no loss in accuracy. Typical computation times are a few minutes for parentage assignment, and a few hours for full pedigree reconstruction when not all individuals are genotyped.
A word of caution: the most likely relationship is not necessarily the true relationship between a pair, due to the random nature of Mendelian segregation, and possible genotyping errors. In addition, the most likely relationship for a pair will not necessarily result in the highest global likelihood, and may therefore not have been assigned.