Configuration

DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)

DeepSomatic v1.7.0, tumour-only, PacBio HiFi: Tumour-only model for the platform (ONT_TUMOR_ONLY, PACBIO_TUMOR_ONLY or WGS_TUMOR_ONLY) with default PoN filtering; Docker image tag 'latest', reported as v1.7.0.

2 evaluations · 14 results

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Evaluations and results

2 evaluations · 14 results. Different protocols are not a single leaderboard.

Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)

Sorted by AUPRC (indel only, tumour-only, 50x tumour coverage) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	AUPRC (indel only, tumour-only, 50x tumour coverage)	AUPRC (SNV only, tumour-only, 50x tumour coverage)	F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	F1 (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)
DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a)	0.142	Not reported	0.161	Not reported	487	Not reported	799	Not reported	0.133	Not reported	0.202	Not reported	123	Not reported
DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a)	Not reported	0.659	Not reported	0.747	Not reported	3,943	Not reported	19,920	Not reported	0.638	Not reported	0.899	Not reported	35,143

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.142 AUPRC (indel only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.161 F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	487 False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	799 False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.133 Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.202 Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	123 True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.659 AUPRC (SNV only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.747 F1 (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	3,943 False negatives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	19,920 False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'FP'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.638 Precision (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'Precision'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.899 Recall (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'Recall'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	35,143 True positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'TP'

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3 source records and release history

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling · Original source · Nature Communications, published 2025-10-31; PMC12579226 full-text XML
ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) · Original source · Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article
ClairS-TO Source Data workbook · Original source · Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article

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Technical metadata and extraction receipts

Stable ID: somatic-clairs-to-20261011-config-deepsomatic-pacbio-hifi

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: DeepSomatic
version: v1.7.0
foundation model eligible: false
parameters: Tumour-only model for the platform (ONT_TUMOR_ONLY, PACBIO_TUMOR_ONLY or WGS_TUMOR_ONLY) with default PoN filtering; Docker image tag 'latest', reported as v1.7.0
access reuse: Public open-source software and released models
source locator: Supplementary Information 'Command lines used'; Supplementary Tables 2 and 7 row labels
provenance note: DeepSomatic as run on PacBio HiFi tumour-only data in the cited comparison.

Related records

configuration of: DeepSomatic
system: DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025)
system: DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025)

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