Configuration

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

ClairS-TO SS v0.4.0, tumour-only, Illumina: Model trained on synthetic tumours only (GIAB HG001/HG002 for ONT; HG003/HG004 for PacBio and Illumina); default panels of normals (gnomAD r2.1, dbSNP v138, 1000 Genomes PoN, CoLoRSdb) 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 SS 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)	0.242	Not reported	0.293	Not reported	384	Not reported	1,210	Not reported	0.215	Not reported	0.463	Not reported	331	Not reported
ClairS-TO SS 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	0.623	Not reported	0.765	Not reported	4,520	Not reported	17,421	Not reported	0.672	Not reported	0.888	Not reported	35,712

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ClairS-TO SS 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)	0.242 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 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 SS', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: ClairS-TO SS 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)	0.293 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 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 SS', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: ClairS-TO SS 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)	384 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 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 SS', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: ClairS-TO SS 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)	1,210 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 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 SS', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: ClairS-TO SS 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 SS 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 SS', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: ClairS-TO SS 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)	0.463 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 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 SS', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: ClairS-TO SS 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)	331 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 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 SS', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: ClairS-TO SS 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)	0.623 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 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 SS', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: ClairS-TO SS 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)	0.765 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 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 SS', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: ClairS-TO SS 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)	4,520 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 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 SS', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: ClairS-TO SS 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)	17,421 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 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 SS', Tumor coverage '50x', Type 'SNV', column 'FP'
Configuration: ClairS-TO SS 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)	0.672 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 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 SS', Tumor coverage '50x', Type 'SNV', column 'Precision'
Configuration: ClairS-TO SS 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)	0.888 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 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 SS', Tumor coverage '50x', Type 'SNV', column 'Recall'
Configuration: ClairS-TO SS 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)	35,712 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 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 SS', 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-ss-illumina

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: ClairS-TO SS
version: v0.4.0
foundation model eligible: false
parameters: Model trained on synthetic tumours only (GIAB HG001/HG002 for ONT; HG003/HG004 for PacBio and Illumina); default panels of normals (gnomAD r2.1, dbSNP v138, 1000 Genomes PoN, CoLoRSdb) 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 SS as run on Illumina tumour-only data in the cited comparison.

Related records

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

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