Protocol

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

Tumour-only somatic SNV 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 SNVs (Chen et al. 2025 Supplementary Table 7a) · Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)

Sorted by AUPRC (SNV 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 (SNV only, tumour-only, 50x tumour coverage)	F1 (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (SNV 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	0.667 (best in column)	0.786 (best in column)	2,938	16,697 (best in column)	0.684 (best in column)	0.925	36,148
DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	0.659	0.747	3,943	19,920	0.638	0.899	35,143
ClairS-TO SS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	0.644	0.785	2,901 (best in column)	16,917	0.681	0.926 (best in column)	36,185 (best in column)
Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	0.558	0.653	5,855	29,409	0.53	0.85	33,231

All 28 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.558 AUPRC (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.653 F1 (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	5,855 False negatives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	29,409 False positives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'FP'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.53 Precision (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'Precision'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.85 Recall (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', column 'Recall'
Configuration: Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	33,231 True positives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'Clair3', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.644 AUPRC (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.785 F1 (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	2,901 False negatives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	16,917 False positives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.681 Precision (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.926 Recall (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	36,185 True positives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.667 AUPRC (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.786 F1 (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	2,938 False negatives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	16,697 False positives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.684 Precision (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.925 Recall (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', 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 SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	36,148 True positives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', column 'TP'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.659 AUPRC (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	0.747 F1 (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	3,943 False negatives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: DeepSomatic v1.7.0, tumour-only, PacBio HiFi (Chen et al. 2025)	Protocol: PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a) Dataset: COLO829 tumour PacBio HiFi Revio WGS (ClairS-TO benchmark)	19,920 False positives (SNV 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 SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-pacbio-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 7a, Dataset 'COLO829', Caller 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'FP'

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 3
External evaluations: 1

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

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

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

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

Download this release (gzip)

Technical metadata and extraction receipts

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

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 'SNV'
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: 39086
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 SNV (Chen et al. 2025)
assessment: ClairS-TO SS on pacbio-colo829 tumour-only SNV (Chen et al. 2025)
assessment: ClairS-TO SSRS on pacbio-colo829 tumour-only SNV (Chen et al. 2025)
assessment: DeepSomatic on pacbio-colo829 tumour-only SNV (Chen et al. 2025)
assessed by: Select a tumour DNA somatic variant-calling workflow

Suggest a correction