Configuration

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

ClairS-TO SSRS v0.4.0, tumour-only, Illumina: 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 Illumina NovaSeq 6000 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, Illumina (Chen et al. 2025)Evaluation	Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b)	0.233	Not reported	0.294	Not reported	382	Not reported	1,215	Not reported	0.215	Not reported	0.466	Not reported	333	Not reported
ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)Evaluation	Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b)	Not reported	0.65	Not reported	0.77	Not reported	5,025	Not reported	16,017	Not reported	0.687	Not reported	0.875	Not reported	35,207

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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, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.233 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 illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.294 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 illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	382 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 illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	1,215 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 illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.215 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 illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.466 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 illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	333 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 illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.65 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 illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.77 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 illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	5,025 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 illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	16,017 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 illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', column 'FP'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.687 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 illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', column 'Precision'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.875 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 illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, Dataset 'COLO829', Caller 'ClairS-TO SSRS', Tumor coverage '50x', Type 'SNV', column 'Recall'
Configuration: ClairS-TO SSRS v0.4.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	35,207 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 illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-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 7b, 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-illumina

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 Illumina tumour-only data in the cited comparison.

Related records

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

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