Protocol

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

Tumour-only somatic indel 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.

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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 indels (Chen et al. 2025 Supplementary Table 2a) · Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)

Sorted by AUPRC (indel 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 (indel only, tumour-only, 25x tumour coverage)	AUPRC (indel only, tumour-only, 50x tumour coverage)	AUPRC (indel only, tumour-only, 75x tumour coverage)	F1 (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	F1 (indel only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	False negatives (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (indel only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	False positives (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (indel only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	Precision (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (indel only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	Recall (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (indel only, tumour-only, 75x tumour coverage, at the best-F1 threshold)	True positives (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold)	True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (indel 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	0.187 (best in column)	0.202 (best in column)	0.206 (best in column)	0.271 (best in column)	0.282 (best in column)	0.292 (best in column)	318	295 (best in column)	282 (best in column)	1,119 (best in column)	1,179	1,188	0.193 (best in column)	0.197 (best in column)	0.203 (best in column)	0.456	0.496 (best in column)	0.518 (best in column)	267	290 (best in column)	303 (best in column)
ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)Evaluation	0.167	0.183	0.186	0.267	0.28	0.28	305 (best in column)	299	300	1,234	1,171	1,168	0.185	0.196	0.196	0.479 (best in column)	0.489	0.487	280 (best in column)	286	285
Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)Evaluation	0.0675	0.104	0.106	0.141	0.191	0.196	376	373	392	2,161	1,419	1,189	0.0882	0.13	0.14	0.357	0.362	0.33	209	212	193
DeepSomatic v1.7.0, tumour-only, ONT (Chen et al. 2025)Evaluation	0.0644	0.0992	0.119	0.0929	0.117	0.123	463	506	504	1,920	688 (best in column)	647 (best in column)	0.0597	0.103	0.111	0.208	0.135	0.139	122	79	81

All 84 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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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 indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.0675 AUPRC (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'Indel', column 'AUPRC'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.141 F1 (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'Indel', column 'F1-score'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	376 False negatives (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'Indel', column 'FN'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	2,161 False positives (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'Indel', column 'FP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.0882 Precision (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'Indel', column 'Precision'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.357 Recall (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'Indel', column 'Recall'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	209 True positives (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '25x', Type 'Indel', column 'TP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.104 AUPRC (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.191 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	373 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	1,419 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.13 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.362 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	212 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	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.106 AUPRC (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'Indel', column 'AUPRC'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.196 F1 (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'Indel', column 'F1-score'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	392 False negatives (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'Indel', column 'FN'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	1,189 False positives (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'Indel', column 'FP'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.14 Precision (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'Indel', column 'Precision'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.33 Recall (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'Indel', column 'Recall'
Configuration: Clair3 v1.0.8, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	193 True positives (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '75x', Type 'Indel', 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 indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.167 AUPRC (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', 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 indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.267 F1 (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', 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 indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	305 False negatives (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', 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 indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	1,234 False positives (indel 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 Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-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 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', 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-indel

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 'Indel'
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: 585
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 Indel (Chen et al. 2025)
assessment: ClairS-TO SS on ont-colo829 tumour-only Indel (Chen et al. 2025)
assessment: ClairS-TO SSRS on ont-colo829 tumour-only Indel (Chen et al. 2025)
assessment: DeepSomatic on ont-colo829 tumour-only Indel (Chen et al. 2025)
assessed by: Select a tumour DNA somatic variant-calling workflow

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