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 October 13, 2025)
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Small variant benchmark from a complete assembly of X and Y chromosomes
Published
Author(s)
, , , Lindsay Harris, Chunlin Xiao, Fritz Sedlazeck, Kishwar Shafin, Andrew Carroll,
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
Pub Type
Journals
Download Paper
Keywords
benchmark, human genome, variant calling, de novo assembly, reference material
Citation
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Created January 8, 2025, Updated March 4, 2025