Journal article

YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data

Fan Zhang, Ruoyan Chen, Dongbing Liu, Xiaotian Yao, Guoqing Li, Yabin Jin, Chang Yu, Yingrui Li, Lachlan JM Coin



BACKGROUND: Y haplogroup analyses are an important component of genealogical reconstruction, population genetic analyses, medical genetics and forensics. These fields are increasingly moving towards use of low-coverage, high throughput sequencing. While there have been methods recently proposed for assignment of Y haplogroups on the basis of high-coverage sequence data, assignment on the basis of low-coverage data remains challenging. RESULTS: We developed a new algorithm, YHap, which uses an imputation framework to jointly predict Y chromosome genotypes and assign Y haplogroups using low coverage population sequence data. We use data from the 1000 genomes project to demonstrate that YHap pr..

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University of Melbourne Researchers


Awarded by National Basic Research Program of China (973 program)

Awarded by Chinese 863 program

Awarded by National Natural Science Foundation of China

Awarded by ARC

Funding Acknowledgements

This study is mainly supported by the National Basic Research Program of China (973 program no. 2011CB809201, 2011CB809202, 2011CB809203), the Chinese 863 program (2012AA02A201), the National Natural Science Foundation of China (30890032, 31161130357). LJMC is supported by an ARC Future Fellowship no. FT110100972.