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.
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. https://doi.org/10.1186/1471-2105-14-331
If you find errors, please report here.