MatchY: A software implementation of pedigree-based calculation of Y-STR match probabilities

Y-STRs are used in forensic genetics to investigate male trace material in cases where no useful autosomal STR profiles can be established. While non-matching suspects can be safely excluded from trace donorship this way, interpreting Y-STR haplotype matches is less straightforward. Equating the corresponding Y-STR match probabilities to haplotype frequencies estimated from population databases is not only common practice, but is also recommended by the International Society for Forensic Genetics. However, this approach ignores that population databases, in principle, cannot be representative of all plausible alternative suspects in each and every case. Therefore, we previously introduced a novel mathematical framework for calculating Y-STR match probabilities drawing upon the suspect's male pedigree, thereby obviating the use of haplotype frequency estimates from population databases for this purpose. Here, we present the implementation of this framework into a publicly available software tool, named MatchY. Expanding the original approach in various ways, the tool can handle any number of single or multi-copy Y-STRs with known mutation rates and allowing both one-step and two-step mutations. MatchY can calculate match probabilities for pedigrees of any size and complexity based upon the haplotype information of its typed members, while simulating haplotypes of untyped ones. In addition to considering all plausible trace donor candidates within the pedigree, the tool can also consider a hypothetical, most closely related candidate from outside the pedigree. The performance of MatchY has been tested using various marker sets and example pedigrees. Together, these features make MatchY a practical and formally correct tool for the interpretation of Y-STR matches by calculating Y-STR match probabilities based on the suspect's male pedigree.