Aardvark: sifting through differences in a mound of variants

Genome biology 2026 Open access

Read full text
Authors: James Holt, Zev N. Kronenberg, Christopher T. Saunders, Egor Dolzhenko, Peter Krusche, Nathan D. Olson, Justin M. Zook, Michael A. Eberle
DOI: 10.1186/s13059-026-04165-0
Cited by: 1
References: 21

Abstract

Abstract Variant benchmarking is critical in assessing the accuracy of genomic secondary pipelines. However, traditional benchmarking tools that require exact genotype matches inject biases from variant representation and are ill-suited for tandem repeat or structural variation. We describe Aardvark, a variant benchmarking tool that introduces the basepair score to directly compare haplotype sequences, reducing representation biases while allowing for partial credit scoring. The tool also includes a traditional genotype score and supports separate or joint benchmarking of small variants, tandem repeats, and structural variants (

Fields of Study & Subjects

Genetic Associations and Epidemiology Genomics and Rare Diseases Genomics and Phylogenetic Studies

Publication details

Journal / source
Genome biology
Publisher
Springer Science and Business Media LLC
Volume
27
Issue
1
Publication date
18 June 2026
Language
EN