Protocol

ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a)

Tumour-only somatic SNV calling scored by AUPRC and by precision, recall and F1 at the best-F1 threshold, with TP, FP and FN counts.

4 evaluations · 84 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

4 recorded evaluations, 84 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

4 evaluations · 84 results. Different protocols are not a single leaderboard.

Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) · Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)

Sorted by AUPRC (SNV only, tumour-only, 25x 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	AUPRC (SNV only, tumour-only, 25x tumour coverage)	AUPRC (SNV only, tumour-only, 50x tumour coverage)	AUPRC (SNV only, tumour-only, 75x tumour coverage)	F1 (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	F1 (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	F1 (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	False negatives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	False negatives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	False positives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	Precision (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	Precision (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	Recall (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	Recall (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	True positives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	True positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold)
ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)Evaluation	0.649 (best in column)	0.663 (best in column)	0.668 (best in column)	0.767 (best in column)	0.768 (best in column)	0.767 (best in column)	3,523	3,142	3,171	17,187 (best in column)	17,605 (best in column)	17,651 (best in column)	0.664 (best in column)	0.661 (best in column)	0.661 (best in column)	0.906	0.916	0.915	34,010	34,391	34,362
ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)Evaluation	0.615	0.618	0.619	0.763	0.764	0.763	3,245 (best in column)	2,696 (best in column)	2,723 (best in column)	18,015	18,870	18,951	0.656	0.649	0.647	0.913 (best in column)	0.928 (best in column)	0.927 (best in column)	34,288 (best in column)	34,837 (best in column)	34,810 (best in column)
DeepSomatic v1.7.0, tumour-only, ONT (Chen et al. 2025)Evaluation	0.603	0.633	0.636	0.703	0.725	0.718	4,528	3,165	3,531	23,387	22,978	23,124	0.585	0.599	0.595	0.879	0.916	0.906	33,005	34,368	34,002
Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)Evaluation	0.554	0.569	0.559	0.683	0.713	0.703	7,056	6,342	7,087	21,236	18,804	18,647	0.589	0.624	0.62	0.812	0.831	0.811	30,477	31,191	30,446

All 84 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.554 AUPRC (SNV only, tumour-only, 25x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'SNV', column 'AUPRC'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.683 F1 (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'SNV', column 'F1-score'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	7,056 False negatives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'SNV', column 'FN'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	21,236 False positives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'SNV', column 'FP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.589 Precision (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'SNV', column 'Precision'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.812 Recall (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'SNV', column 'Recall'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	30,477 True positives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'SNV', column 'TP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.569 AUPRC (SNV only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.713 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	6,342 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	18,804 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'FP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.624 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'Precision'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.831 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'Recall'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	31,191 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'TP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.559 AUPRC (SNV only, tumour-only, 75x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'SNV', column 'AUPRC'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.703 F1 (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'SNV', column 'F1-score'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	7,087 False negatives (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'SNV', column 'FN'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	18,647 False positives (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'SNV', column 'FP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.62 Precision (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'SNV', column 'Precision'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.811 Recall (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'SNV', column 'Recall'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	30,446 True positives (SNV only, tumour-only, 75x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'SNV', column 'TP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.615 AUPRC (SNV only, tumour-only, 25x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'SNV', column 'AUPRC'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.763 F1 (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'SNV', column 'F1-score'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	3,245 False negatives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'SNV', column 'FN'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	18,015 False positives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'SNV', column 'FP'

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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-protocol-ont-colo829-snv

areas: dna-genomes
contexts: clinical_research
protocol: Each caller is run on the tumour BAM alone; calls are compared with the filtered cell-line truth set using som.py (hap.py 0.3.12) and ClairS-TO compare_vcf, which the authors cross-checked. Precision, recall and F1 are reported at the quality threshold giving the best F1.
version: Supplementary Table 2a, Type 'SNV'
metric: f1-score
limitations: Developer paper: the authors developed ClairS-TO and its SS and SSRS models (author_reported); Clair3, also run here, comes from the same group. Comparators were run by the authors with their recommended settings.; Tumour-only calling of cell lines; the truth sets were derived from tumour-normal data and are filtered to variants with coverage at least 4, at least 3 alternative reads and VAF at least 0.05, so very low-VAF variants are not scored.; Precision, recall and F1 are at the best achievable F1 over the caller's quality threshold, chosen on the test data (Figure 2 legend); AUPRC summarises the whole curve. Neither is an operating point fixed in advance.; Clair3 is a germline caller; its calls were treated as somatic after removing those tagged by ClairS-TO's panels of normals.; Single sample per dataset; no interval estimates.; Comparator versions are old relative to the paper (DeepSomatic 1.7.0 run from the 'latest' container; Mutect2 4.2.6.1; Octopus 0.7.4; Pisces 5.3.0).; Competing interests: the senior author (R.L.) receives research funding from ONT.; Whether the DeepSomatic 1.7.0 models were trained with COLO829 data is not stated in the source.; The denominator is TP + FN after the authors' truth filter; it is the same for every caller in this table.
denominator: 37533
source locator: Supplementary Table 2a; Results 'Benchmarking datasets and evaluation'; Methods 'Benchmarking'; Supplementary Information 'Command lines used'

Related records

uses data: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)
assessment: Clair3 on ont-colo829 tumour-only SNV (Chen et al. 2025)
assessment: ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025)
assessment: ClairS-TO SSRS on ont-colo829 tumour-only SNV (Chen et al. 2025)
assessment: DeepSomatic on ont-colo829 tumour-only SNV (Chen et al. 2025)
assessed by: Select a tumour DNA somatic variant-calling workflow

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