Challenges in somatic variant calling include a lack of long-read variant callers and of publicly available benchmarking datasets. We developed DeepSomatic, a somatic variant caller for short- and long-read technologies, and created seven somatic variant benchmarks derived from cancer cell lines, which we make available as a public database: CASTLE-panel.
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References
Fang, L. T. et al. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nat. Biotechnol. 39, 1151–1160 (2021). This paper presents a somatic variant benchmark for a breast cancer cell line.
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Keskus, A. G. et al. Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing. Nat. Biotechnol. https://doi.org/10.1038/s41587-025-02618-8 (2025). This paper presents Severus, a long-read-based structural variant caller.
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This is a summary of: Park, J. et al. Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic. Nat. Biotechnol. https://doi.org/10.1038/s41587-025-02839-x (2025).
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Improving somatic variant calling with long-read technologies and public datasets. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02860-0
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DOI: https://doi.org/10.1038/s41587-025-02860-0
