Configuration

Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)

Clair3 v1.0.8, tumour-only, PacBio HiFi: Germline caller run on the tumour BAM (ONT model r1041_e82_400bps_sup_v420); calls tagged by ClairS-TO's panels of normals removed, the rest treated as somatic.

2 evaluations · 14 results

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Evaluations and results

2 evaluations · 14 results. Different protocols are not a single leaderboard.

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	Protocol and dataset	AUPRC (indel only, tumour-only, 50x tumour coverage)	AUPRC (SNV only, tumour-only, 50x tumour coverage)	F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	F1 (SNV 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 negatives (SNV 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)	False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (indel 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 (indel 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 (indel 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)
Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a)	0.137	Not reported	0.2	Not reported	377	Not reported	1,482	Not reported	0.136	Not reported	0.382	Not reported	233	Not reported
Clair3 v1.0.8, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	PacBio HiFi COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7a)	Not reported	0.558	Not reported	0.653	Not reported	5,855	Not reported	29,409	Not reported	0.53	Not reported	0.85	Not reported	33,231

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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: 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'

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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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Technical metadata and extraction receipts

Stable ID: somatic-clairs-to-20261011-config-clair3-pacbio-hifi

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: Clair3
version: v1.0.8
foundation model eligible: false
parameters: Germline caller run on the tumour BAM (ONT model r1041_e82_400bps_sup_v420); calls tagged by ClairS-TO's panels of normals removed, the rest treated as somatic
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: Clair3 as run on PacBio HiFi tumour-only data in the cited comparison.

Related records

configuration of: Clair3
system: Clair3 on pacbio-colo829 tumour-only Indel (Chen et al. 2025)
system: Clair3 on pacbio-colo829 tumour-only SNV (Chen et al. 2025)

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