Small variant benchmark from a complete assembly of X and Y chromosomes
Abstract
Abstract The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant detection on male sex chromosomes X and Y, we create a small variant benchmark set with 111,725 variants for the Genome in a Bottle HG002 reference material. We develop an active evaluation approach to demonstrate the benchmark set reliably identifies errors in challenging genomic regions and across short and long read callsets. We show how complete assemblies can expand benchmarks to difficult regions, but highlight remaining challenges benchmarking variants in long homopolymers and tandem repeats, complex gene conversions, copy number variable gene arrays, and human satellites.
Article Details
Authors (27)
Justin Wagner
Nathan D. Olson
Jennifer McDaniel
Lindsay Harris
Brendan J. Pinto
David Jáspez
Adrián Muñoz-Barrera
Luis A. Rubio-Rodríguez
José M. Lorenzo-Salazar
Carlos Flores
Sayed Mohammad Ebrahim Sahraeian
Giuseppe Narzisi
Marta Byrska-Bishop
Uday S. Evani
Chunlin Xiao
Juniper A. Lake
Peter Fontana
Craig Greenberg
Donald Freed
Mohammed Faizal Eeman Mootor
Paul C. Boutros
Lisa Murray
Kishwar Shafin
Andrew Carroll
Fritz J. Sedlazeck
Melissa Wilson
Justin M. Zook