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A unified haplotype-based method for accurate and comprehensive variant calling

Nature Biotechnology volume 39, pages 885–892 (2021)Cite this article

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Abstract

Almost all haplotype-based variant callers were designed specifically for detecting common germline variation in diploid populations, and give suboptimal results in other scenarios. Here we present Octopus, a variant caller that uses a polymorphic Bayesian genotyping model capable of modeling sequencing data from a range of experimental designs within a unified haplotype-aware framework. Octopus combines sequencing reads and prior information to phase-called genotypes of arbitrary ploidy, including those with somatic mutations. We show that Octopus accurately calls germline variants in individuals, including single nucleotide variants, indels and small complex replacements such as microinversions. Using a synthetic tumor data set derived from clean sequencing data from a sample with known germline haplotypes and observed mutations in a large cohort of tumor samples, we show that Octopus is more sensitive to low-frequency somatic variation, yet calls considerably fewer false positives than other methods. Octopus also outputs realigned evidence BAM files to aid validation and interpretation.

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Fig. 1: Overview of the unified haplotype-based algorithm, showing joint calling of two samples with the population calling model.
Fig. 2: Germline variant calling accuracy.
Fig. 3: Overview of synthetic-tumor creation.
Fig. 4: Somatic mutation calling accuracy with a paired normal sample.
Fig. 5: Somatic mutation calling accuracy in synthetic PACA tumors without a paired normal sample for various sequencing depths.

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Data availability

All germline data used in this manuscript are publicly available from GIAB, Precision FDA and ENA. Links are provided in Supplementary Note 1. Trio data from the WGS500 project are available from the European Nucleotide Archive under accession no. PRJEB9151 (samples AW_SC_4654, AW_SC_4655 and AW_SC_4659). The synthetic-tumor data have been deposited in the Sequence Read Archive under BioProject accession no. PRJNA694520. The corresponding truth sets have been deposited to figshare (https://doi.org/10.6084/m9.figshare.13902212).

Code availability

Octopus source code and documentation is freely available under the MIT licence from https://github.com/luntergroup/octopus. Custom code used for data analysis is available from https://github.com/luntergroup/octopus-paper.

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Acknowledgements

This work was supported by The Wellcome Trust Genomic Medicine and Statistics PhD Program (grant nos. 203735/Z/16/Z to D.P.C.). The computational aspects of this research were supported by the Wellcome Trust Core Award grant number 203141/Z/16/Z and the NIHR Oxford BRC. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health.

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Authors and Affiliations

  1. MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK

    Daniel P. Cooke & Gerton Lunter

  2. Manchester Cancer Research Centre, University of Manchester, Manchester, UK

    David C. Wedge

  3. Department of Epidemiology, University Medical Centre Groningen, Groningen, the Netherlands

    Gerton Lunter

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  1. Daniel P. Cooke
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  2. David C. Wedge
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  3. Gerton Lunter
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Contributions

D.P.C. and G.L. designed the algorithm and wrote the manuscript. D.P.C. implemented the algorithm and performed the evaluation. D.C.W. provided data for the synthetic tumors and critically reviewed the manuscript.

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Correspondence to Daniel P. Cooke.

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The authors declare no competing interests.

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Peer review information Nature Biotechnology thanks Federico Abascal and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary Information

Supplementary Figs. 1–6, Tables 1–4 and Notes 1–4.

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Cooke, D.P., Wedge, D.C. & Lunter, G. A unified haplotype-based method for accurate and comprehensive variant calling. Nat Biotechnol 39, 885–892 (2021). https://doi.org/10.1038/s41587-021-00861-3

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