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

Published

Author(s)

Justin Wagner, Nathanael Olson, Jennifer McDaniel, Lindsay Harris, Chunlin Xiao, Fritz Sedlazeck, Kishwar Shafin, Andrew Carroll, Justin Zook

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.
Citation
Nature Communications
Volume
16

Keywords

benchmark, human genome, variant calling, de novo assembly, reference material

Citation

Wagner, J. , Olson, N. , McDaniel, J. , Harris, L. , Xiao, C. , Sedlazeck, F. , Shafin, K. , Carroll, A. and Zook, J. (2025), Small variant benchmark from a complete assembly of X and Y chromosomes, Nature Communications, [online], https://doi.org/10.1038/s41467-024-55710-z, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=956904 (Accessed March 19, 2025)

Issues

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Created January 8, 2025, Updated March 4, 2025