Configuration

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

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

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)
ClairS-TO SSRS v0.4.0, tumour-only, PacBio HiFi (Chen et al. 2025)Evaluation	PacBio HiFi COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7a)	0.197	Not reported	0.262	Not reported	341	Not reported	1,174	Not reported	0.186	Not reported	0.441	Not reported	269	Not reported
ClairS-TO SSRS v0.4.0, 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	0.667	Not reported	0.786	Not reported	2,938	Not reported	16,697	Not reported	0.684	Not reported	0.925	Not reported	36,148

All 14 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, 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: 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'

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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-clairs-to-ssrs-pacbio-hifi

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: ClairS-TO SSRS
version: v0.4.0
foundation model eligible: false
parameters: SS model fine-tuned on four real cancer cell lines (HCC1937, HCC1954, H1437, H2009); default panels of normals and hard filters; short-read runs omit long-read-specific filters
access reuse: Public open-source software and released models
source locator: Supplementary Information 'Command lines used'; Supplementary Tables 2 and 7 row labels
provenance note: ClairS-TO SSRS as run on PacBio HiFi tumour-only data in the cited comparison.

Related records

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

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