Configuration

ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)

ClairS-TO SSRS v0.4.0, tumour-only, ONT: SS model fine-tuned on four real cancer cell lines (HCC1937, HCC1954, H1437, H2009); default panels of normals and hard filters; short-read runs omit long-read-specific filters.

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.

Evaluations and results

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

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)
ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)Evaluation	ONT HCC1395 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2b), HCC1395 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.4 (best in column)	0.427 (best in column)	0.44 (best in column)	Not reported	Not reported	Not reported	0.444 (best in column)	0.508 (best in column)	0.539 (best in column)	Not reported	Not reported	Not reported	786	650	591	Not reported	Not reported	Not reported	639 (best in column)	715 (best in column)	715 (best in column)	Not reported	Not reported	Not reported	0.471 (best in column)	0.497 (best in column)	0.517 (best in column)	Not reported	Not reported	Not reported	0.42	0.521 (best in column)	0.564 (best in column)	Not reported	Not reported	Not reported	570 (best in column)	706 (best in column)	765 (best in column)	Not reported	Not reported	Not reported
ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)Evaluation	ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a), COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.187	0.202	0.206	Not reported	Not reported	Not reported	0.271	0.282	0.292	Not reported	Not reported	Not reported	318 (best in column)	295 (best in column)	282 (best in column)	Not reported	Not reported	Not reported	1,119	1,179	1,188	Not reported	Not reported	Not reported	0.193	0.197	0.203	Not reported	Not reported	Not reported	0.456 (best in column)	0.496	0.518	Not reported	Not reported	Not reported	267	290	303	Not reported	Not reported	Not reported
ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)Evaluation	ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a), COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	Not reported	Not reported	Not reported	0.649 (best in column)	0.663 (best in column)	0.668 (best in column)	Not reported	Not reported	Not reported	0.767	0.768	0.767	Not reported	Not reported	Not reported	3,523 (best in column)	3,142 (best in column)	3,171	Not reported	Not reported	Not reported	17,187	17,605	17,651	Not reported	Not reported	Not reported	0.664	0.661	0.661	Not reported	Not reported	Not reported	0.906 (best in column)	0.916 (best in column)	0.915 (best in column)	Not reported	Not reported	Not reported	34,010 (best in column)	34,391 (best in column)	34,362 (best in column)
ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)Evaluation	ONT HCC1395 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2b), HCC1395 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	Not reported	Not reported	Not reported	0.579	0.599	0.601	Not reported	Not reported	Not reported	0.768 (best in column)	0.794 (best in column)	0.799 (best in column)	Not reported	Not reported	Not reported	5,023	3,319	3,071 (best in column)	Not reported	Not reported	Not reported	11,444 (best in column)	11,643 (best in column)	11,617 (best in column)	Not reported	Not reported	Not reported	0.704 (best in column)	0.713 (best in column)	0.715 (best in column)	Not reported	Not reported	Not reported	0.844	0.897	0.905	Not reported	Not reported	Not reported	27,189	28,893	29,141

All 84 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ClairS-TO SSRS 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)	0.187 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 SSRS 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 SSRS', Tumor coverage '25x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SSRS 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)	0.271 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 SSRS 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 SSRS', Tumor coverage '25x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SSRS 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)	318 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 SSRS 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 SSRS', Tumor coverage '25x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SSRS 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)	1,119 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 SSRS 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 SSRS', Tumor coverage '25x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SSRS 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)	0.193 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '25x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SSRS 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)	0.456 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '25x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SSRS 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)	267 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '25x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SSRS 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)	0.202 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SSRS 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)	0.282 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SSRS 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)	295 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SSRS 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)	1,179 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SSRS 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)	0.197 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SSRS 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)	0.496 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SSRS 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)	290 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SSRS 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)	0.206 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '75x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SSRS 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)	0.292 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '75x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SSRS 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)	282 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '75x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SSRS 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)	1,188 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '75x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SSRS 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)	0.203 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '75x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SSRS 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)	0.518 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '75x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SSRS 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)	303 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 ClairS-TO SSRS 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 SSRS', Tumor coverage '75x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.649 AUPRC (SNV only, tumour-only, 25x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SSRS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '25x', Type 'SNV', column 'AUPRC'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.767 F1 (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SSRS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '25x', Type 'SNV', column 'F1-score'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	3,523 False negatives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SSRS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '25x', Type 'SNV', column 'FN'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	17,187 False positives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SSRS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', 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-clairs-to-ssrs-ont

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: ClairS-TO SSRS
version: v0.4.0
foundation model eligible: false
parameters: SS model fine-tuned on four real cancer cell lines (HCC1937, HCC1954, H1437, H2009); default panels of normals and hard filters; short-read runs omit long-read-specific filters
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: ClairS-TO SSRS as run on ONT tumour-only data in the cited comparison.

Related records

configuration of: ClairS-TO
system: ClairS-TO SSRS on ont-colo829 tumour-only Indel (Chen et al. 2025)
system: ClairS-TO SSRS on ont-colo829 tumour-only SNV (Chen et al. 2025)
system: ClairS-TO SSRS on ont-hcc1395 tumour-only Indel (Chen et al. 2025)
system: ClairS-TO SSRS on ont-hcc1395 tumour-only SNV (Chen et al. 2025)

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