biostudies-literatureUnknown14Zhang F<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, 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.<h4>Conclusions</h4>BMC bioinformatics331https://www.ebi.ac.uk/biostudies/studies/S-EPMC4225519biostudies-literatureYHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data.PMC4225519Li GZhang FLi YYu CCoin LJLiu DYao XJin YChen RfalseYHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data.<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, 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.<h4>Conclusions</h4>2013-01-01T00:00:00Z2013 Nov2026-05-02T09:45:16.681Z2026-04-07T17:53:06.252ZS-EPMC42255192425217110.1186/1471-2105-14-331