VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements

Inversions, duplications, and other critical medically challenging variations are often ignored by routine genetic analyses. This is due to the complexity of these alleles but also because of the inability to accurately align them with state-of-the-art methods. We introduce VACmap, a novel non-linear long-read mapping method designed to improve detection of these difficult genomic regions, including critical genes like LPA and GBA1, which are significant risk factors for cardiovascular disease and Parkinson’s disease, respectively.