Simultaneous Phasing of Multiple Polyploids

摘要

We address the problem of phasing polyploids specifically with polyploidy larger than two. We consider the scenario where the input is the genotype of samples along a genie chromosomal segment. In this setting, instead of NGS reads of the segments of a sample, genotype data from multiple individuals is available for simultaneous phasing. For this mathematically interesting problem, with application in plant genomics, we design and test two algorithms under a parsimony model. The first is a linear time greedy algorithm and the second is a more carefully crafted algebraic algorithm. We show that both the methods work reasonably well (with accuracy on an average larger than 80%). The former is very time-efficient and the latter improves the accuracy further.