ybyra: Y-chromosome haplogroup calling using a tree-based scoring method

Abstract

We present ybyra, a Snakemake workflow for automated Y-chromosome haplogroup assignment using a tree-based scoring method with robust and transparent heuristics. The pipeline supports both human reference genome builds 37 and 38, makes use of three different well-curated Y-SNP tree topologies and features an optional ancient DNA damage filter to accommodate low-coverage degraded samples. ybyra produces reproducible, scalable haplogroup calls with detailed scoring outputs to facilitate quality assessment and reporting. We further showcase its versatility by applying it to horse Y-chromosome data, highlighting its applicability beyond humans. Availabilityybyra is published under the MIT license and freely available at github.com/tpinotti/ybyra.