Published comparison transcribed from the pinned source; not reproduced.
1 evaluation · 6 results. Different protocols are not a single leaderboard.
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)
Sorted by False negatives (SNV only, synthetic WES) (lower 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 | False negatives (SNV only, synthetic WES) | False positives (SNV only, synthetic WES) | Precision (SNV only, synthetic WES) | Recall (SNV only, synthetic WES) | True positives (SNV only, synthetic WES) | Count (SNV only, synthetic WES, total filtered calls) |
|---|---|---|---|---|---|---|
| FreeBayes 1.3.6 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)Evaluation | 2314 | 1 | 1 | 0.452 | 1908 | 1909 |
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Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1)
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Not reported Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Single pair Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version Not reported Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs Synthetic tumour and normal WES BAMs Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: metric implementation Match of PASS SNV calls to the inserted SNV list Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: population 4,709 inserted SNVs Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: protocol id somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: split Single synthetic pair Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Origin independent_paper Context-only references | Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Table 1, row 'FreeBayes' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: somatic-wes-synthetic-20261011-eval-freebayes-bamsurgeon-wes-snv