PhyloImpute - phylogeny-aware genotype imputation methods for Y-chromosomal DNA

Genotype imputation is relevant for increasing the genetic variants available from forensic or ancient samples with low quantity and quality of DNA and from targeted sequencing approaches, enabling meta-analysis to reach the required statistical power or to establish allele frequencies. Current genotype imputation tools are based on the co-inheritance of SNPs on shared haplotype segments of recombining DNA and are therefore not suited for non-recombining DNA. Imputation for non-recombining DNA, such as the human Y chromosome, would allow expansion of information from lower-cost targeted approaches to reach data quantities comparable to massively parallel sequencing-derived data. We introduce PhyloImpute, an easy-to-use software that leverage the phylogenetic nature of Y-chromosomal SNPs provided in (custom) phylogenetic trees to impute missing genetic variants. PhyloImpute characterizes samples by predicting haplogroups more accurately than state-of-the-art predictor tools, identifies deviations from the expected phylogeny, and establishes and illustrates haplotype frequencies on maps. PhyloImpute is licensed under GPL-3.0. The command line tool, extensive instructions and test data are freely available at https://github.com/ZehraKoksal/PhyloImpute. The graphical user interface tool for windows and linux with a tutorial and test data are freely available at https://zenodo.org/records/17950955.