Configuration

DeepSomatic v1.7.0, tumour-only, Illumina (Chen et al. 2025)

DeepSomatic v1.7.0, tumour-only, Illumina: Tumour-only model for the platform (ONT_TUMOR_ONLY, PACBIO_TUMOR_ONLY or WGS_TUMOR_ONLY) with default PoN filtering; Docker image tag 'latest', reported as v1.7.0.

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)
DeepSomatic v1.7.0, tumour-only, Illumina (Chen et al. 2025)Evaluation	Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b)	0.0521	Not reported	0.0788	Not reported	607	Not reported	1,919	Not reported	0.0533	Not reported	0.151	Not reported	108	Not reported
DeepSomatic v1.7.0, tumour-only, Illumina (Chen et al. 2025)Evaluation	Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b)	Not reported	0.504	Not reported	0.619	Not reported	14,968	Not reported	16,151	Not reported	0.61	Not reported	0.628	Not reported	25,264

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DeepSomatic v1.7.0, 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)	0.0521 AUPRC (indel 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 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, 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)	0.0788 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: DeepSomatic v1.7.0, 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)	607 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: DeepSomatic v1.7.0, 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)	1,919 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: DeepSomatic v1.7.0, 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)	0.0533 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: DeepSomatic v1.7.0, 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)	0.151 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: DeepSomatic v1.7.0, 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)	108 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: DeepSomatic v1.7.0, 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)	0.504 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 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 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: DeepSomatic v1.7.0, 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)	0.619 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 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 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: DeepSomatic v1.7.0, 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)	14,968 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 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 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: DeepSomatic v1.7.0, 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)	16,151 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 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 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'FP'
Configuration: DeepSomatic v1.7.0, 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)	0.61 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'Precision'
Configuration: DeepSomatic v1.7.0, 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)	0.628 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'Recall'
Configuration: DeepSomatic v1.7.0, 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)	25,264 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	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Tumor coverage '50x', Type 'SNV', column 'TP'

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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-deepsomatic-illumina

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: DeepSomatic
version: v1.7.0
foundation model eligible: false
parameters: Tumour-only model for the platform (ONT_TUMOR_ONLY, PACBIO_TUMOR_ONLY or WGS_TUMOR_ONLY) with default PoN filtering; Docker image tag 'latest', reported as v1.7.0
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: DeepSomatic as run on Illumina tumour-only data in the cited comparison.

Related records

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

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