Dataset

COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)

COLO829 metastatic melanoma cell line, tumour reads only, Oxford Nanopore R10.4.1, 101.8x, subsampled to 75x, 50x and 25x.

Evaluation results

8 evaluations · 168 results. Different protocols are not a single leaderboard.

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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: 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'

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Assay ONT R10.4.1 WGS (EPI2ME Labs), minimap2 to GRCh38 Context-only references	ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `6b5e5262df96467010d539e919c7a52aac3e49c616b3eeb403d1865dcb173b8a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay ONT R10.4.1 WGS (EPI2ME Labs), minimap2 to GRCh38 Context-only references	ClairS-TO Source Data workbook Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article Retrieved: 2026-10-11T21:38:10Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `4347c74fe0ce2ed04b1ac40d28bd4f8885c77f628e911a7027a275b1234828f8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay ONT R10.4.1 WGS (EPI2ME Labs), minimap2 to GRCh38 Context-only references	ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article Retrieved: 2026-10-11T21:37:53Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `806cd47423031495bf00543d7e3e3abad3f93fc4ee3ee2a7a570c335227f5603` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population One cancer cell line, tumour sample only (no matched normal used by the callers) Context-only references	ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `6b5e5262df96467010d539e919c7a52aac3e49c616b3eeb403d1865dcb173b8a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population One cancer cell line, tumour sample only (no matched normal used by the callers) Context-only references	ClairS-TO Source Data workbook Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article Retrieved: 2026-10-11T21:38:10Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `4347c74fe0ce2ed04b1ac40d28bd4f8885c77f628e911a7027a275b1234828f8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population One cancer cell line, tumour sample only (no matched normal used by the callers) Context-only references	ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article Retrieved: 2026-10-11T21:37:53Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `806cd47423031495bf00543d7e3e3abad3f93fc4ee3ee2a7a570c335227f5603` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Scope note Truth: NYGC COLO829 somatic truth (42,993 SNVs, 985 indels before filtering); a truth variant is kept only if coverage is at least 4, at least 3 reads support the alternative allele and VAF is at least 0.05 Context-only references	ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.scope_note` Source artifact SHA-256: `6b5e5262df96467010d539e919c7a52aac3e49c616b3eeb403d1865dcb173b8a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Scope note Truth: NYGC COLO829 somatic truth (42,993 SNVs, 985 indels before filtering); a truth variant is kept only if coverage is at least 4, at least 3 reads support the alternative allele and VAF is at least 0.05 Context-only references	ClairS-TO Source Data workbook Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article Retrieved: 2026-10-11T21:38:10Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.scope_note` Source artifact SHA-256: `4347c74fe0ce2ed04b1ac40d28bd4f8885c77f628e911a7027a275b1234828f8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Scope note Truth: NYGC COLO829 somatic truth (42,993 SNVs, 985 indels before filtering); a truth variant is kept only if coverage is at least 4, at least 3 reads support the alternative allele and VAF is at least 0.05 Context-only references	ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article Retrieved: 2026-10-11T21:37:53Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.scope_note` Source artifact SHA-256: `806cd47423031495bf00543d7e3e3abad3f93fc4ee3ee2a7a570c335227f5603` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Context-only references	ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Original source ↗ Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `6b5e5262df96467010d539e919c7a52aac3e49c616b3eeb403d1865dcb173b8a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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-data-ont-colo829

areas: dna-genomes
contexts: clinical_research
population: One cancer cell line, tumour sample only (no matched normal used by the callers)
assay: ONT R10.4.1 WGS (EPI2ME Labs), minimap2 to GRCh38
split: Held out from ClairS-TO training (SS: synthetic HG001/HG002 or HG003/HG004; SSRS: plus HCC1937, HCC1954, H1437 and H2009)
scope note: Truth: NYGC COLO829 somatic truth (42,993 SNVs, 985 indels before filtering); a truth variant is kept only if coverage is at least 4, at least 3 reads support the alternative allele and VAF is at least 0.05
source locator: Results 'Benchmarking datasets and evaluation' paragraph 1; Supplementary Table 1a
missing metadata: version: reason: unreported; note: Data releases are named by provider only

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