Dataset

BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)

Synthetic whole-exome tumour-normal pair: 4,709 of 10,000 randomly selected COSMIC SNVs inserted with BAMSurgeon 1.4.1 into a variant-free BAM; the paired germline BAM has no inserted mutations.

Evaluation results

3 evaluations · 18 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: FreeBayes 1.3.6 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2310 False negatives (SNV only, synthetic WES) 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 the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'FreeBayes', column 'FN'
Configuration: FreeBayes 1.3.6 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1 False positives (SNV only, synthetic WES) 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 the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'FreeBayes', column 'FP'
Configuration: FreeBayes 1.3.6 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1 Precision (SNV only, synthetic WES) 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 the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'FreeBayes', column 'Precision'
Configuration: FreeBayes 1.3.6 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	0.452 Recall (SNV only, synthetic WES) 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 the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'FreeBayes', column 'Recall'
Configuration: FreeBayes 1.3.6 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1910 Count (SNV only, synthetic WES, total filtered calls) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'FreeBayes', column 'Total Query'
Configuration: FreeBayes 1.3.6 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1910 True positives (SNV only, synthetic WES) 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 the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'FreeBayes', column 'TP'
Configuration: Mutect2 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1740 False negatives (SNV only, synthetic WES) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Mutect2', column 'FN'
Configuration: Mutect2 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	4 False positives (SNV only, synthetic WES) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Mutect2', column 'FP'
Configuration: Mutect2 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	0.999 Precision (SNV only, synthetic WES) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Mutect2', column 'Precision'
Configuration: Mutect2 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	0.631 Recall (SNV only, synthetic WES) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Mutect2', column 'Recall'
Configuration: Mutect2 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2980 Count (SNV only, synthetic WES, total PASS calls) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Mutect2', column 'Total Query'
Configuration: Mutect2 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2970 True positives (SNV only, synthetic WES) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Mutect2', column 'TP'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2530 False negatives (SNV only, synthetic WES) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'FN'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1 False positives (SNV only, synthetic WES) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'FP'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1 Precision (SNV only, synthetic WES) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'Precision'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	0.463 Recall (SNV only, synthetic WES) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'Recall'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2180 Count (SNV only, synthetic WES, total PASS calls) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'Total Query'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2180 True positives (SNV only, synthetic WES) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'TP'

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6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Assay Synthetic WES BAMs processed with nf-core/sarek 3.5.0 (BWA-MEM, GRCh38) Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs' and 2.4 'Variant Calling and Bioinformatic Workflow'; Table 1 'Total Truth' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML Retrieved: 2026-10-11T21:37:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population One synthetic tumour-normal pair; 4,709 inserted SNVs (BAMSurgeon parameters --mindepth 50 --maxdepth 500 --minmutreads 5) Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs' and 2.4 'Variant Calling and Bioinformatic Workflow'; Table 1 'Total Truth' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML Retrieved: 2026-10-11T21:37:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs' and 2.4 'Variant Calling and Bioinformatic Workflow'; Table 1 'Total Truth' Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs' and 2.4 'Variant Calling and Bioinformatic Workflow'; Table 1 'Total Truth' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML Retrieved: 2026-10-11T21:37:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split Single synthetic evaluation sample Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs' and 2.4 'Variant Calling and Bioinformatic Workflow'; Table 1 'Total Truth' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML Retrieved: 2026-10-11T21:37:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Synthetic whole-exome tumour-normal pair: 4,709 of 10,000 randomly selected COSMIC SNVs inserted with BAMSurgeon 1.4.1 into a variant-free BAM; the paired germline BAM has no inserted mutations. Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs' and 2.4 'Variant Calling and Bioinformatic Workflow'; Table 1 'Total Truth' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML Retrieved: 2026-10-11T21:37:40Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025) Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs' and 2.4 'Variant Calling and Bioinformatic Workflow'; Table 1 'Total Truth' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML Retrieved: 2026-10-11T21:37:40Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Original source · Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML

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Technical metadata and extraction receipts

Stable ID: somatic-wes-synthetic-20261011-data-bamsurgeon-wes

areas: dna-genomes
contexts: clinical_research
population: One synthetic tumour-normal pair; 4,709 inserted SNVs (BAMSurgeon parameters --mindepth 50 --maxdepth 500 --minmutreads 5)
assay: Synthetic WES BAMs processed with nf-core/sarek 3.5.0 (BWA-MEM, GRCh38)
split: Single synthetic evaluation sample
source locator: Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs' and 2.4 'Variant Calling and Bioinformatic Workflow'; Table 1 'Total Truth'
missing metadata: accession: reason: unavailable; note: Synthetic data available from the corresponding author on request (Data Availability Statement); version: reason: unreported

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