2014/07/30 by Luke Jostins, Yali Xu, Jostins, Luke +11
Biochemistry, Genetics and Molecular Biology · #FOS: Biological sciences #Forensic and Genetic Research #Genetic Associations and Epidemiology #Genetic diversity and population structure #Genomics (q-bio.GN) #Populations and Evolution (q-bio.PE)
paper · pdf · doi:10.48550/arxiv.1407.7988
openalex publication_date 2014/07/30 · openalex created_date 2016/06/24 · openalex updated_date 2026/07/28
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 http://sourceforge.net/projects/yfitter/