Protocol

PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a)

Tumour-only somatic indel calling scored by AUPRC and by precision, recall and F1 at the best-F1 threshold, with TP, FP and FN counts.

4 evaluations · 28 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

4 recorded evaluations, 28 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

4 evaluations · 28 results. Different protocols are not a single leaderboard.

Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) · Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)

Sorted by AUPRC (indel only, tumour-only, 50x tumour coverage) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	AUPRC (indel only, tumour-only, 50x tumour coverage)	F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)
ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	0.197 (best in column)	0.262 (best in column)	341	1,174	0.186 (best in column)	0.441	269
ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	0.189	0.262	308 (best in column)	1,396	0.178	0.495 (best in column)	302 (best in column)
DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	0.142	0.161	487	799 (best in column)	0.133	0.202	123
Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	0.137	0.2	377	1,482	0.136	0.382	233

All 28 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.137 AUPRC (indel only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.2 F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	377 False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	1,482 False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.136 Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.382 Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	233 True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.189 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.262 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	308 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	1,396 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.178 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.495 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	302 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.197 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.262 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	341 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	1,174 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.186 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.441 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	269 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.142 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.161 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	487 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	799 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 pacbio-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'FP'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

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Sources and history

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

3 source records and release history

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

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Technical metadata and extraction receipts

Stable ID: somatic-clairs-to-20261011-protocol-pacbio-colo829-indel

areas: dna-genomes
contexts: clinical_research
protocol: Each caller is run on the tumour BAM alone; calls are compared with the filtered cell-line truth set using som.py (hap.py 0.3.12) and ClairS-TO compare_vcf, which the authors cross-checked. Precision, recall and F1 are reported at the quality threshold giving the best F1.
version: Supplementary Table 7a, Type 'Indel'
metric: f1-score
limitations: Developer paper: the authors developed ClairS-TO and its SS and SSRS models (author_reported); Clair3, also run here, comes from the same group. Comparators were run by the authors with their recommended settings.; Tumour-only calling of cell lines; the truth sets were derived from tumour-normal data and are filtered to variants with coverage at least 4, at least 3 alternative reads and VAF at least 0.05, so very low-VAF variants are not scored.; Precision, recall and F1 are at the best achievable F1 over the caller's quality threshold, chosen on the test data (Figure 2 legend); AUPRC summarises the whole curve. Neither is an operating point fixed in advance.; Clair3 is a germline caller; its calls were treated as somatic after removing those tagged by ClairS-TO's panels of normals.; Single sample per dataset; no interval estimates.; Comparator versions are old relative to the paper (DeepSomatic 1.7.0 run from the 'latest' container; Mutect2 4.2.6.1; Octopus 0.7.4; Pisces 5.3.0).; Competing interests: the senior author (R.L.) receives research funding from ONT.; Whether the DeepSomatic 1.7.0 models were trained with COLO829 data is not stated in the source.; The denominator is TP + FN after the authors' truth filter; it is the same for every caller in this table.
denominator: 610
source locator: Supplementary Table 7a; Results 'Benchmarking datasets and evaluation'; Methods 'Benchmarking'; Supplementary Information 'Command lines used'

Related records

uses data: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)
assessment: Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025)
assessment: ClairS-TO SS on pacbio-colo829 tumour-only Indel (Chen et al. 2025)
assessment: ClairS-TO SSRS on pacbio-colo829 tumour-only Indel (Chen et al. 2025)
assessment: DeepSomatic on pacbio-colo829 tumour-only Indel (Chen et al. 2025)
assessed by: Select a tumour DNA somatic variant-calling workflow

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