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.
Competing Interest Statement
JAL is an employee of PacBio. DF is an employee of Sentieon, Inc., and holds stock options as part of the standard compensation package. PCB sits on the Scientific Advisory Boards of Intersect Diagnostics Inc., Sage Bionetworks and BioSymetrics Inc. LM is an employee and shareholder of Illumina Inc. KS and AC are employees of Google LLC and own Alphabet stock as part of the standard compensation package. FJS has support from ONT, Illumina, Pacbio and Genentech.
Footnotes
Shortening and minor updates to text
