Configuration

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

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

2 evaluations · 42 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.

Evaluations and results

2 evaluations · 42 results. Different protocols are not a single leaderboard.

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	Protocol and dataset	AUPRC (indel only, tumour-only, 25x tumour coverage)	AUPRC (indel only, tumour-only, 50x tumour coverage)	AUPRC (indel only, tumour-only, 75x tumour coverage)	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 (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)	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 (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 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 (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)	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 (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)	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 (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)	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 (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)	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)
DeepSomatic v1.7.0, tumour-only, ONT (Chen et al. 2025)Evaluation	ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a)	0.0644	0.0992	0.119	Not reported	Not reported	Not reported	0.0929	0.117	0.123	Not reported	Not reported	Not reported	463	506	504	Not reported	Not reported	Not reported	1,920	688	647	Not reported	Not reported	Not reported	0.0597	0.103	0.111	Not reported	Not reported	Not reported	0.208	0.135	0.139	Not reported	Not reported	Not reported	122	79	81	Not reported	Not reported	Not reported
DeepSomatic v1.7.0, tumour-only, ONT (Chen et al. 2025)Evaluation	ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a)	Not reported	Not reported	Not reported	0.603	0.633	0.636	Not reported	Not reported	Not reported	0.703	0.725	0.718	Not reported	Not reported	Not reported	4,528	3,165	3,531	Not reported	Not reported	Not reported	23,387	22,978	23,124	Not reported	Not reported	Not reported	0.585	0.599	0.595	Not reported	Not reported	Not reported	0.879	0.916	0.906	Not reported	Not reported	Not reported	33,005	34,368	34,002

All 42 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: DeepSomatic v1.7.0, 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)	0.0644 AUPRC (indel only, tumour-only, 25x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '25x', Type 'Indel', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, 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)	0.0929 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'Indel', column 'F1-score'
Configuration: DeepSomatic v1.7.0, 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)	463 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'Indel', column 'FN'
Configuration: DeepSomatic v1.7.0, 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)	1,920 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'Indel', column 'FP'
Configuration: DeepSomatic v1.7.0, 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)	0.0597 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'Indel', column 'Precision'
Configuration: DeepSomatic v1.7.0, 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)	0.208 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'Indel', column 'Recall'
Configuration: DeepSomatic v1.7.0, 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)	122 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'Indel', column 'TP'
Configuration: DeepSomatic v1.7.0, 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)	0.0992 AUPRC (indel only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, 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)	0.117 F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: DeepSomatic v1.7.0, 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)	506 False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: DeepSomatic v1.7.0, 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)	688 False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: DeepSomatic v1.7.0, 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)	0.103 Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: DeepSomatic v1.7.0, 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)	0.135 Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: DeepSomatic v1.7.0, 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)	79 True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: DeepSomatic v1.7.0, 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)	0.119 AUPRC (indel only, tumour-only, 75x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '75x', Type 'Indel', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, 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)	0.123 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '75x', Type 'Indel', column 'F1-score'
Configuration: DeepSomatic v1.7.0, 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)	504 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '75x', Type 'Indel', column 'FN'
Configuration: DeepSomatic v1.7.0, 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)	647 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '75x', Type 'Indel', column 'FP'
Configuration: DeepSomatic v1.7.0, 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)	0.111 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '75x', Type 'Indel', column 'Precision'
Configuration: DeepSomatic v1.7.0, 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)	0.139 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '75x', Type 'Indel', column 'Recall'
Configuration: DeepSomatic v1.7.0, 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)	81 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '75x', Type 'Indel', column 'TP'
Configuration: DeepSomatic v1.7.0, 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)	0.603 AUPRC (SNV only, tumour-only, 25x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on 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 'DeepSomatic', Tumor coverage '25x', Type 'SNV', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, 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)	0.703 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'SNV', column 'F1-score'
Configuration: DeepSomatic v1.7.0, 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)	4,528 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'SNV', column 'FN'
Configuration: DeepSomatic v1.7.0, 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)	23,387 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '25x', Type 'SNV', column 'FP'

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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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Stable ID: somatic-clairs-to-20261011-config-deepsomatic-ont

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

Related records

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

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