Small variant benchmark from a complete assembly of X and Y chromosomes

Wagner, J.; Olson, N. D.; McDaniel, J.; Harris, L.; Pinto, B. J.; Jaspez, D.; Munoz-Barrera, A.; Rubio-Rodriguez, L. A.; Lorenzo-Salazar, J. M.; Flores, C.; Sahraeian, S. M. E.; Narzisi, G.; Byrska-Bishop, M.; Evani, U. S.; Xiao, C.; Lake, J. A.; Fontana, P.; Greenberg, C.; Freed, D.; Boutros, P. C.; Mootor, M. F. E.; Murray, L.; Shafin, K.; Carroll, A.; Sedlazeck, F. J.; Wilson, M.; Zook, J. M.; Genome in a Bottle Consortium,

The sex chromosomes contain complex, important genes impacting medical phenotypes. This benchmark includes 111,725 variants across the Genome in a Bottle HG002 reference material, advancing variant accuracy across the X and Y chromosomes. This work demonstrates how complete assemblies can expand benchmarks to more difficult regions, while highlighting remaining challenges in variant benchmarking in complex genomic regions such as gene conversions, copy number variable gene arrays, and human satellites.