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Published in:
2020 | OriginalPaper | Chapter
Simultaneous Phasing of Multiple Polyploids
Authors : Laxmi Parida, Filippo Utro
Published in: Computational Intelligence Methods for Bioinformatics and Biostatistics
Publisher: Springer International Publishing
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Abstract
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 genic 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.