Result

True positives (SNV only, synthetic WES) of FreeBayes 1.3.6 via nf-core/sarek 3.5.0 (López-Cade et al. 2025) on BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)

1910 True positives (SNV only, synthetic WES)

Methods

Tested 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)
Procedure: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1)
Evaluation: FreeBayes on the synthetic WES pair (López-Cade et al. 2025)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedComparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'FreeBayes', column 'TP'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Single synthetic pair
Adaptation: Not reported
Scoring implementation: Match of PASS SNV calls to the inserted SNV list

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

1 evidence row 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
Reported result 1908 Individual claims	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ Table 1, row 'FreeBayes', column 'TP' Version: Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML Retrieved: 2026-10-11T21:37:40Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-11 independent paper Audit details Extraction: Parsed table-wrap 'Table 1' of the pinned article XML with extract/extract_wes_synthetic.py; header and caller labels asserted. Table 1, row 'FreeBayes', column 'TP' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md (docs/reviews/use-cases/tumour-dna-somatic-variant-detection-2026-10-11.md). Field: `attributes.printed_value` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Extraction artifact

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Sources and history

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

1 source record and release history

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-result-freebayes-bamsurgeon-wes-snv-tp

metric: true-positive-count
metric direction: higher
unit: count
printed value: 1908
source locator: Table 1, row 'FreeBayes', column 'TP'
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Independent re-retrieval and hash check; reviewer's own parser compared every table cell; stratified hand check against the rendered table or quoted sentence.; reviewer: claude; reviewer note: Claude research agent reviewer-onc-1, independent of the extractor uc-oncology; no human review claimed; date: 2026-10-11; artifact sha256: 0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12650410/fullTextXML; note: Extraction: Parsed table-wrap 'Table 1' of the pinned article XML with extract/extract_wes_synthetic.py; header and caller labels asserted. Table 1, row 'FreeBayes', column 'TP' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md (docs/reviews/use-cases/tumour-dna-somatic-variant-detection-2026-10-11.md).
numeric value: 1908
metric qualifier: SNV only, synthetic WES
unit detail: counted entity: inserted SNVs called
missing metadata: uncertainty: reason: unreported

Related records

evaluation: FreeBayes on the synthetic WES pair (López-Cade et al. 2025)

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