Configuration

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

ClairS-TO SS v0.4.0, tumour-only, ONT: Model trained on synthetic tumours only (GIAB HG001/HG002 for ONT; HG003/HG004 for PacBio and Illumina); default panels of normals (gnomAD r2.1, dbSNP v138, 1000 Genomes PoN, CoLoRSdb) 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 SS 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)	0.407 (best in column)	0.416 (best in column)	0.434 (best in column)	Not reported	Not reported	Not reported	0.448 (best in column)	0.512 (best in column)	0.533 (best in column)	Not reported	Not reported	Not reported	826	463	433	Not reported	Not reported	Not reported	479 (best in column)	1,241	1,185	Not reported	Not reported	Not reported	0.525 (best in column)	0.418 (best in column)	0.438 (best in column)	Not reported	Not reported	Not reported	0.391	0.659 (best in column)	0.681 (best in column)	Not reported	Not reported	Not reported	530 (best in column)	893 (best in column)	923 (best in column)	Not reported	Not reported	Not reported
ClairS-TO SS 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)	0.167	0.183	0.186	Not reported	Not reported	Not reported	0.267	0.28	0.28	Not reported	Not reported	Not reported	305 (best in column)	299 (best in column)	300 (best in column)	Not reported	Not reported	Not reported	1,234	1,171 (best in column)	1,168 (best in column)	Not reported	Not reported	Not reported	0.185	0.196	0.196	Not reported	Not reported	Not reported	0.479 (best in column)	0.489	0.487	Not reported	Not reported	Not reported	280	286	285	Not reported	Not reported	Not reported
ClairS-TO SS 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	0.615 (best in column)	0.618 (best in column)	0.619 (best in column)	Not reported	Not reported	Not reported	0.763 (best in column)	0.764	0.763	Not reported	Not reported	Not reported	3,245 (best in column)	2,696 (best in column)	2,723	Not reported	Not reported	Not reported	18,015	18,870	18,951	Not reported	Not reported	Not reported	0.656	0.649	0.647	Not reported	Not reported	Not reported	0.913 (best in column)	0.928 (best in column)	0.927 (best in column)	Not reported	Not reported	Not reported	34,288 (best in column)	34,837 (best in column)	34,810 (best in column)
ClairS-TO SS 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	0.569	0.586	0.59	Not reported	Not reported	Not reported	0.763	0.793 (best in column)	0.797 (best in column)	Not reported	Not reported	Not reported	4,713	3,008	2,478 (best in column)	Not reported	Not reported	Not reported	12,371 (best in column)	12,239 (best in column)	12,663 (best in column)	Not reported	Not reported	Not reported	0.69 (best in column)	0.705 (best in column)	0.701 (best in column)	Not reported	Not reported	Not reported	0.854	0.907	0.923	Not reported	Not reported	Not reported	27,499	29,204	29,734

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 SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.167 AUPRC (indel only, tumour-only, 25x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.267 F1 (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	305 False negatives (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	1,234 False positives (indel only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.185 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.479 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	280 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.183 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.28 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	299 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	1,171 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.196 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.489 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	286 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.186 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '75x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.28 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '75x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	300 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '75x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	1,168 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '75x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.196 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '75x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.487 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '75x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic indels (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	285 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 SS on ont-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '75x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.615 AUPRC (SNV only, tumour-only, 25x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'SNV', column 'AUPRC'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	0.763 F1 (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'SNV', column 'F1-score'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	3,245 False negatives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'SNV', column 'FN'
Configuration: ClairS-TO SS v0.4.0, tumour-only, ONT (Chen et al. 2025)	Protocol: ONT COLO829 tumour-only, 25x to 75x, somatic SNVs (Chen et al. 2025 Supplementary Table 2a) Dataset: COLO829 tumour ONT R10.4.1 WGS (ClairS-TO benchmark)	18,015 False positives (SNV only, tumour-only, 25x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ClairS-TO SS on ont-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-ont-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 2a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '25x', Type 'SNV', column 'FP'

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3 source records and release history

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling · Original source · Nature Communications, published 2025-10-31; PMC12579226 full-text XML
ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) · Original source · Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article
ClairS-TO Source Data workbook · Original source · Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article

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

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: ClairS-TO SS
version: v0.4.0
foundation model eligible: false
parameters: Model trained on synthetic tumours only (GIAB HG001/HG002 for ONT; HG003/HG004 for PacBio and Illumina); default panels of normals (gnomAD r2.1, dbSNP v138, 1000 Genomes PoN, CoLoRSdb) 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 SS as run on ONT tumour-only data in the cited comparison.

Related records

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

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