Dataset Information

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

ABSTRACT: 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 provides accurate Y haplogroup assignment with less than 2x coverage. CONCLUSIONS: Borrowing information across multiple samples within a population using an imputation framework enables accurate Y haplogroup assignment.

SUBMITTER: Zhang F

PROVIDER: S-EPMC4225519 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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

Zhang Fan F Chen Ruoyan R Liu Dongbing D Yao Xiaotian X Li Guoqing G Jin Yabin Y Yu Chang C Li Yingrui Y Coin Lachlan J M LJ

BMC bioinformatics 20131119

<h4>Background</h4>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.<h4>Results</h4>We developed a new algorithm, YHap, whi ...[more]

PMID: 24252171

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Dataset Information

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

Publications

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

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