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Exploring the limit of using a deep neural network on pileup data for germline variant calling

Nature Machine Intelligence volume 2, pages 220–227 (2020)Cite this article

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A preprint version of the article is available at bioRxiv.

Abstract

Single-molecule sequencing technologies have emerged in recent years and revolutionized structural variant calling, complex genome assembly and epigenetic mark detection. However, the lack of a highly accurate small variant caller has limited these technologies from being more widely used. Here, we present Clair, the successor to Clairvoyante, a program for fast and accurate germline small variant calling, using single-molecule sequencing data. For Oxford Nanopore Technology data, Clair achieves better precision, recall and speed than several competing programs, including Clairvoyante, Longshot and Medaka. Through studying the missed variants and benchmarking intentionally overfitted models, we found that Clair may be approaching the limit of possible accuracy for germline small variant calling using pileup data and deep neural networks. Clair requires only a conventional central processing unit (CPU) for variant calling and is an open-source project available at https://github.com/HKU-BAL/Clair.

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Fig. 1: Clair network architecture and layer details.
Fig. 2: ONT benchmarking results for SNPs and indels.
Fig. 3: The category distribution of FPs and FNs made by Clair in the 1:168×|2:64× experiment on ONT data and six genome browser screen captures showing examples of different categories.

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Data availability

The details of and links to the reference genomes, truth variants, ONT data, PacBio CCS data and Illumina data that support the findings of this study are available in the ‘Data sources’ section of the Supplementary Notes. The variant call format files generated by Clair in this study are available at http://www.bio8.cs.hku.hk/clair_models/VCFBenchmarked/.

Code availability

Clair is open source, and available at https://github.com/HKU-BAL/Clair. Clair is licensed under the BSD 3-Clause licence.

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Acknowledgements

We thank S. Salzberg, M. Schatz and F. Sedlazeck for comments. R.L. was supported by the ECS (grant number 27204518) of the HKSAR government, and by the URC fund at HKU. T.-W.L., C.-L.W., Y.-S.W., C.-I.T., C.-M. Liu and C.-M. Leung were supported by the ITF (grant number ITF/331/17FP) from the Innovation and Technology Commission, HKSAR government.

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Authors and Affiliations

  1. Department of Computer Science, The University of Hong Kong, Hong Kong, China

    Ruibang Luo, Chak-Lim Wong, Yat-Sing Wong, Chi-Ian Tang, Chi-Man Liu, Chi-Ming Leung & Tak-Wah Lam

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  1. Ruibang Luo
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Contributions

R.L. and T.-W.L. conceived the study. R.L, C.-L.W., Y.-S.W., C.-I.T., C.-M. Liu and C.-M. Leung analysed the data and wrote the paper.

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Correspondence to Ruibang Luo or Tak-Wah Lam.

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Supplementary information

Supplementary Information

Supplementary Notes, Supplementary Tables 1-6, Supplementary Figure 1

Supplementary Table

The details of the FP and FN results in ONT experiment 1:168x|2:64x

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Luo, R., Wong, CL., Wong, YS. et al. Exploring the limit of using a deep neural network on pileup data for germline variant calling. Nat Mach Intell 2, 220–227 (2020). https://doi.org/10.1038/s42256-020-0167-4

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