Variant Benchmarking Tools

Offers methods for robustly checking variant call accuracy

Many genetic tests used today for studying and treating diseases look at tens to hundreds of genes. The test results usually include a list of “variant calls,” which point out variations in the genetic code. Often these arrive in the Variant Call Format (VCF) developed by the GA4GH Large-Scale Genomics (LSG) Work Stream.

Ensuring variant calls are accurate — for example, without false negatives or positives — matters for diagnosing and treating patients and learning more about diseases. The GA4GH Variant Benchmarking Tools offer methods for avoiding common pitfalls and achieving standard metrics when benchmarking variant calls.

Robust benchmarking for variant calls is essential to the work of government agencies, academic bioinformatics researchers, clinical laboratories, sequencing technology developers, and commercial technology and bioinformatics developers. Representatives from each of these groups shaped the development of the tools.

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  • Assess variant calls from next-generation sequencing with robust accuracy
  • Avoid common pitfalls and misinterpretations with performance metrics

Target users

Researchers, clinical laboratories, data generators, funding agencies, developers, and research institutes

Community resources

Dive deeper into this product!  Standardised benchmarking methods and tools are essential to robust accuracy assessment of next generation sequencing variant calling. Benchmarking variant calls requires careful attention to definitions of performance metrics, sophisticated comparison approaches, and stratification by variant type and genome context. The germline small variant benchmarking tools address challenges in matching variant calls with different representations; defining standard performance metrics; enabling stratification of performance by variant type and genome context; and developing and describing limitations of high-confidence calls and regions that can be used as “truth.” The GA4GH Variant Benchmarking Tools have been piloted in the precisionFDA variant calling challenges to identify the best-in-class variant calling methods within high-confidence regions.

Don't see your name? Get in touch:

  • Kaushik Ghose
    Seven Bridges Genomics, Inc.
  • Andrew Jesaitis
    Ginkgo Bioworks
  • Stephen Keenan
    Wellcome Sanger Institute (WSI)
  • Peter Krusche
  • Tom Morris
    Curoverse, Inc.
  • Len Trigg
    Real Time Genomics
  • Justin Zook
    National Institute of Standards and Technology