Dataset

SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions

Validation sample in Guille et al. 2025.

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Evaluation results

33 evaluations · 198 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.812 f1-score 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-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H32; Tools 'DeepSomatic-WES'; column 'F1'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	10 false-positive-count 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-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), E32; Tools 'DeepSomatic-WES'; column 'FP'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	6.64e-8 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), G32; Tools 'DeepSomatic-WES'; column 'FPR'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.804 precision 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-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I32; Tools 'DeepSomatic-WES'; column 'PPV'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.82 recall 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-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), F32; Tools 'DeepSomatic-WES'; column 'TPR'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	41 true-positive-count 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-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), D32; Tools 'DeepSomatic-WES'; column 'TP'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.901 f1-score 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-WES on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H17; Tools 'DeepSomatic-WES'; column 'F1'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	34 false-positive-count 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-WES on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), E17; Tools 'DeepSomatic-WES'; column 'FP'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	2.26e-7 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic-WES on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), G17; Tools 'DeepSomatic-WES'; column 'FPR'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.966 precision 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-WES on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I17; Tools 'DeepSomatic-WES'; column 'PPV'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.843 recall 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-WES on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), F17; Tools 'DeepSomatic-WES'; column 'TPR'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	978 true-positive-count 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-WES on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), D17; Tools 'DeepSomatic-WES'; column 'TP'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.178 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H22; Tools 'FreeBayes'; column 'F1'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	226 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), E22; Tools 'FreeBayes'; column 'FP'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.0000015 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), G22; Tools 'FreeBayes'; column 'FPR'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.107 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I22; Tools 'FreeBayes'; column 'PPV'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.54 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), F22; Tools 'FreeBayes'; column 'TPR'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	27 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), D22; Tools 'FreeBayes'; column 'TP'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.596 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H4; Tools 'FreeBayes'; column 'F1'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	883 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), E4; Tools 'FreeBayes'; column 'FP'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.00000586 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), G4; Tools 'FreeBayes'; column 'FPR'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.496 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I4; Tools 'FreeBayes'; column 'PPV'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.748 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), F4; Tools 'FreeBayes'; column 'TPR'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	868 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), D4; Tools 'FreeBayes'; column 'TP'
Configuration: Lancet 1.1.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.463 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lancet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H31; Tools 'Lancet'; column 'F1'

Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

8 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-8cc1db47c7f9
Property and statement	Original source and location	Review and provenance
attributes.accession SRA run SRR7890879 (Methods), in experiment SRX4728489 (Table 2) Context-only references	A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Original source ↗ Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML Retrieved: 2026-10-09T19:56:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.accession` Source artifact SHA-256: `2c6fc6f329f7ebea34889de5f0cc8dff2d0d90b9a8dc3192ddac0949281c9827` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.assay WES, Illumina HiSeq 4000 per Table 2 (Methods: 76x sample from a different platform, Fudan University); 76x; duplication rate 23.49% Context-only references	A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Original source ↗ Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML Retrieved: 2026-10-09T19:56:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `2c6fc6f329f7ebea34889de5f0cc8dff2d0d90b9a8dc3192ddac0949281c9827` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.context HCC1395 triple-negative breast cancer cell line with HCC1395BL matched normal; SEQC2 high-confidence somatic call set restricted to high-confidence regions Context-only references	A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Original source ↗ Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML Retrieved: 2026-10-09T19:56:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.context` Source artifact SHA-256: `2c6fc6f329f7ebea34889de5f0cc8dff2d0d90b9a8dc3192ddac0949281c9827` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population Truth: 1160 SNVs and 50 indels (Table 2; Table S7 column P) Context-only references	A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Original source ↗ Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML Retrieved: 2026-10-09T19:56:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `2c6fc6f329f7ebea34889de5f0cc8dff2d0d90b9a8dc3192ddac0949281c9827` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Context-only references	A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Original source ↗ Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML Retrieved: 2026-10-09T19:56:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `2c6fc6f329f7ebea34889de5f0cc8dff2d0d90b9a8dc3192ddac0949281c9827` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.split Validation sample not used to select the ensembles; it is a second WES replicate (Fudan University) of the same HCC1395/HCC1395BL pair and the same SEQC2 truth set as the development sample SRR7890883 (Table 2 row 'SEQC2') Context-only references	A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Original source ↗ Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML Retrieved: 2026-10-09T19:56:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `2c6fc6f329f7ebea34889de5f0cc8dff2d0d90b9a8dc3192ddac0949281c9827` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
description Validation sample in Guille et al. 2025. Context-only references	A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Original source ↗ Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML Retrieved: 2026-10-09T19:56:52Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `2c6fc6f329f7ebea34889de5f0cc8dff2d0d90b9a8dc3192ddac0949281c9827` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
name SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions Context-only references	A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Original source ↗ Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset' Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML Retrieved: 2026-10-09T19:56:52Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `2c6fc6f329f7ebea34889de5f0cc8dff2d0d90b9a8dc3192ddac0949281c9827` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

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A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing · Original source · Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML

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Stable ID: somatic-20261009-data-guille2025-seqc2-fd-wes

areas: dna-genomes
contexts: clinical_research
assay: WES, Illumina HiSeq 4000 per Table 2 (Methods: 76x sample from a different platform, Fudan University); 76x; duplication rate 23.49%
accession: SRA run SRR7890879 (Methods), in experiment SRX4728489 (Table 2)
context: HCC1395 triple-negative breast cancer cell line with HCC1395BL matched normal; SEQC2 high-confidence somatic call set restricted to high-confidence regions
population: Truth: 1160 SNVs and 50 indels (Table 2; Table S7 column P)
split: Validation sample not used to select the ensembles; it is a second WES replicate (Fudan University) of the same HCC1395/HCC1395BL pair and the same SEQC2 truth set as the development sample SRR7890883 (Table 2 row 'SEQC2')
source locator: Table 2 row 'SEQC2-FD'; Methods 'SEQC2 dataset'
missing metadata: population detail: reason: unreported; note: Matched normal run for the validation sample and the post-alignment procedure used for Table S7 are not stated; version: reason: unreported; note: Methods point to the SEQC2 'release/latest' folder; the call-set version is not printed

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