Aardvark: sifting through differences in a mound of variants

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 the traditional genotype score and supports separate or joint benchmarking of small variants, tandem repeats, and structural variants (<10 kb). Aardvark accepts standard inputs, runs $$\approx$$ ≈ 18x faster than hap.py, and is open source ( https://github.com/PacificBiosciences/aardvark or https://doi.org/10.5281/zenodo.20271610 ).