YFitter: Maximum likelihood assignment of Y chromosome haplogroups from low-coverage sequence data

YFitter: Maximum likelihood assignment of Y chromosome haplogroups from low-coverage sequence data

Luke Jostins, Yali Xu, Shane McCarthy, Qasim Ayub, Richard Durbin, Jeff Barrett, Chris Tyler-Smith
(Submitted on 30 Jul 2014)

Low-coverage short-read resequencing experiments have the potential to expand our understanding of Y chromosome haplogroups. However, the uncertainty associated with these experiments mean that haplogroups must be assigned probabilistically to avoid false inferences. We propose an efficient dynamic programming algorithm that can assign haplogroups by maximum likelihood, and represent the uncertainty in assignment. We apply this to both genotype and low-coverage sequencing data, and show that it can assign haplogroups accurately and with high resolution. The method is implemented as the program YFitter, which can be downloaded from this http URL

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