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

Abstract

The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To evaluate variant detection on chromosomes X and Y, we created an 111,725 variant benchmark for the Genome in a Bottle HG002 reference material. We show how complete assemblies can expand benchmarks to difficult regions, but highlight remaining challenges benchmarking complex gene conversions, copy number variable gene arrays, and human satellites.