Aardvark

A tool for sniffing out the differences in vari-Ants

Aardvark was built to quickly compare different variant call sets. Key features of Aardvark include:

• Ability to benchmark variants from a "query" set against those from a "truth" set
• Constructs haplotype sequences, allowing for basepair-level comparisons that are variant-type agnostic and that enable implicit partial credit for inexact matching variant calls
• Genotype assessment, allowing for a strict exact-match scoring (similar to traditional metrics)
• Provides output summary statistics and VCF files with annotations
• Ability to merge variants from multiple input sets
• Variants are compared in a haplotype context (sequence level), harmonizing different variant representations
• Multiple merge strategies for different scenarios from strict exact-matching to looser majority-vote schemes
• Quality of life additions: Efficient methods with a fast run-time distributed as a single binary

Authors: Matt Holt, Zev Kronenberg

Availability

• Latest release with binary

Documentation

• Installation instructions
• User guide with quickstart
• Output files
• Recommended settings
• Methods
• Performance

Citation

If you use Aardvark, please cite our bioRxiv pre-print:

Holt, James Matthew, et al. "Aardvark: Sifting through differences in a mound of variants." bioRxiv (2025): 2025-10.

Support information

If you notice any missing features, bugs, or need assistance with analyzing the output of Aardvark, please open a GitHub issue.

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