An open resource for accurately benchmarking small variant and reference calls

Published

April 1, 2019

Author(s)

Justin M. Zook, Jennifer H. McDaniel, Marc L. Salit, Nathanael D. Olson, Justin M. Wagner

Abstract

Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) Consortium, we apply a reproducible, cloud-based pipeline to integrate multiple short- and linked-read sequencing datasets and provide benchmark calls for human genomes. We generate benchmark calls for one previously analyzed GIAB sample, as well as six genomes from the Personal Genome Project. These new genomes have broad, open consent, making this a ‘first of its kind’ resource that is available to the community for multiple downstream applications. We produce 17% more benchmark single nucleotide variations, 176% more indels and 12% larger benchmark regions than previously published GIAB benchmarks. We demonstrate that this benchmark reliably identifies errors in existing callsets and highlight challenges in interpreting performance metrics when using benchmarks that are not perfect or comprehensive. Finally, we identify strengths and weaknesses of callsets by stratifying performance according to variant type and genome context.

Citation

Nature Biotechnology

Volume

37

Pub Type

Journals

Download Paper

https://doi.org/10.1038/s41587-019-0074-6

Keywords

genomics, DNA sequencing, Reference Materials, variant calling, bioinformatics

Citation

Zook, J. , McDaniel, J. , Salit, M. , Olson, N. and Wagner, J. (2019), An open resource for accurately benchmarking small variant and reference calls, Nature Biotechnology, [online], https://doi.org/10.1038/s41587-019-0074-6 (Accessed November 20, 2024)