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YHap is a command-line tool for prediction of Y-chromosome genotypes and assignment of haplogroups. The YHap algorithm uses an imputation framework and works with low coverage sequence data, less than 2X coverage.


Population genetics


  • Operation: Genotyping
  • Input: VCF
  • Output: -
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU Lesser General Public License version 3
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: -
  • Contact: fanzhang _at_
  • Collection: -


Zhang F, Chen R, Liu D, Yao X, Li G, Jin Y, Yu C, Li Y, Coin LJ "YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data." BMC Bioinformatics. 2013 Nov 19;14:331.
PMID: 24252171
PMCID: PMC4225519

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