title: 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.
authors.affiliation: BGI-shenzhen, Shenzhen, China. yuchang@genomics.org.cn.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.forename: Ruoyan
authors.initials: R
authors.lastname: Chen
authors.forename: Dongbing
authors.initials: D
authors.lastname: Liu
authors.forename: Xiaotian
authors.initials: X
authors.lastname: Yao
authors.forename: Guoqing
authors.initials: G
authors.lastname: Li
authors.forename: Yabin
authors.initials: Y
authors.lastname: Jin
authors.forename: Chang
authors.initials: C
authors.lastname: Yu
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Lachlan J M
authors.initials: LJ
authors.lastname: Coin
mesh_terms: D000465:Algorithms; D041322:Chromosomes, Human, Y / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D008297:Male; D009154:Mutation / Q000235:genetics; D011237:Predictive Value of Tests; D011336:Probability; D017422:Sequence Analysis, DNA / Q000379:methods*; D020080:Tandem Repeat Sequences / Q000235:genetics