Evidence claim

Relevance of Synthetic WES tumour-normal SNVs (López-Cade et al. 2025 Table 1) to "Select a tumour DNA somatic variant-calling workflow"

Use case: Select a tumour DNA somatic variant-calling workflow
Assessed by: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1)
Relevance: Proxy evidence
Endpoint: Recall and precision of Mutect2, Strelka2 and FreeBayes PASS SNV calls on a BAMSurgeon synthetic WES tumour-normal pair

Proxy, not direct: the inputs and endpoint match the use case (tumour-normal WES, per-caller precision and recall), but the tumour is synthetic, with SNVs inserted into otherwise clean reads, so precision is near 1 by construction and recall mostly reflects default filtering of inserted low-VAF variants.

2 reviewed evaluations

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.

20 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
Citation locations 1 values source id somatic-wes-synthetic-20261011-source-lopezcade2025 locator Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.citation_locators` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group lopezcade2025-wes-synthetic Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.comparison_group` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Three callers on a synthetic WES pair (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 ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.comparison_title` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results; truth sets, specimens, sequencing and caller versions differ between sources. Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.constraints` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Recall and precision of Mutect2, Strelka2 and FreeBayes PASS SNV calls on a BAMSurgeon synthetic WES tumour-normal pair Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.endpoint` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Excluded evaluations 1 values id somatic-wes-synthetic-20261011-eval-freebayes-bamsurgeon-wes-snv reason Table 1 row is internally inconsistent: TP plus FN is 4,222, not the 4,709 truth variants, and the printed recall uses 4,222 as denominator. Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.excluded_evaluations` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by: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 Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.field` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Headline metric recall Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.headline_metric` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 6 values One synthetic WES pair; BAMSurgeon inserts SNVs into real reads but does not model tumour artefacts, so almost no false positives are expected (Discussion). SNVs only; indels not evaluated. Callers run with nf-core/sarek 3.5.0 defaults and no tuning; no custom panel of normals was specified, and sarek's default GATK GRCh38 panel of normals was applied to Mutect2 (Discussion). Mutect2 is reported as 'version 2.2', which is not a GATK release number; the GATK version is not stated. FreeBayes row is internally inconsistent: TP 1,908 plus FN 2,314 is 4,222, not the 4,709 printed as Total Truth, and the printed recall 0.4519 equals 1,908/4,222, whereas 1,908/4,709 is 0.4052. Mutect2 and Strelka2 rows sum to 4,709. The source does not say which value is wrong. Authors are from the clinical group that generated the patient samples; they did not develop the callers. Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.limitations` Source artifact SHA-256: `0d115f3cebe36ed4a0d078b459f7e083a32ceaa5e447f8eefe2dbde38cae863f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Pinned records 17 values record id somatic-wes-synthetic-20261011-eval-mutect2-bamsurgeon-wes-snv fields status links attributes.origin attributes.comparison sha256 77b5d95d2cd8680e75f13230781f6bc60722ef5b50744dca9eb7d4b96fe4ab4b record id somatic-wes-synthetic-20261011-eval-strelka2-bamsurgeon-wes-snv fields status links attributes.origin attributes.comparison sha256 975b4b49227adab5f8bbd02b0c56f183bccf5badefc926582c9667a13fa705a7 record id somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv fields status name description facets source_ids links attributes sha256 8245560997d66e98af7f39ae9c2ac672564ef6e83bd0b761ff51dbb50ae61fef record id somatic-wes-synthetic-20261011-result-mutect2-bamsurgeon-wes-snv-fn fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 30b4dbe161fd8937749a3f70a2fb6a49ee7ff810dc7d8f2ef5fea227219d42e6 record id somatic-wes-synthetic-20261011-result-mutect2-bamsurgeon-wes-snv-fp fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 571cfb9c71727627bbc57c35a3a5b5c1606212d338ce65c4ae15581f046c6889 record id somatic-wes-synthetic-20261011-result-mutect2-bamsurgeon-wes-snv-precision fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 c18cd016a2dc63155ef0e994179ed7d606ac3c0d4b2b99ff54b8a2e7e327ac19 record id somatic-wes-synthetic-20261011-result-mutect2-bamsurgeon-wes-snv-recall fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 dda2c410c116dabadc073188612ad9b824a27fc9ec452e04083d55566fdaae3a record id somatic-wes-synthetic-20261011-result-mutect2-bamsurgeon-wes-snv-total-query fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 396b5dc31c62d2482bb0bbe379de73cf68291790f5e5068a22eee8b087b9a057 record id somatic-wes-synthetic-20261011-result-mutect2-bamsurgeon-wes-snv-tp fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 0e6cf4de8ed151d2bca8041f3177ded552010b72c3544c7a798167b9a316910c record id somatic-wes-synthetic-20261011-result-strelka2-bamsurgeon-wes-snv-fn fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 c95f2cf8ec00ca326ed8b3f12bfdd38fd6b6502f0346b3d53a3c07c8469f990c record id somatic-wes-synthetic-20261011-result-strelka2-bamsurgeon-wes-snv-fp fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 dbdc9fedb461466cb9c22bd299ca1b161ce87760185220a567e2e3c7471d59ec record id somatic-wes-synthetic-20261011-result-strelka2-bamsurgeon-wes-snv-precision fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 5f8d743e93d80ce6d04e775121bdfb81411676512b314259e4651c85217a3a85 record id somatic-wes-synthetic-20261011-result-strelka2-bamsurgeon-wes-snv-recall fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 6c1b0dac202b560defeb8ea5fec4194cfe9dc1607986779b1c8d36bc4393381c record id somatic-wes-synthetic-20261011-result-strelka2-bamsurgeon-wes-snv-total-query fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 7191dd3ffff7071ada6a9310666260f34d5251d1ae146086eb844c34357f91ab record id somatic-wes-synthetic-20261011-result-strelka2-bamsurgeon-wes-snv-tp fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 72adc0f3d0d7ac1a71d5b5bf3691387035066eaa20faef788829955a9770018d record id somatic-wes-synthetic-20261011-source-lopezcade2025 fields status attributes.artifact_sha256 sha256 06416bfa5b7adfb684e8992660894a34ca262314400e662db59cbf313fb3b3a6 record id use-case-tumour-dna-somatic-variant-detection fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 d36ba2079efa58ea91132fc20f54c4982a2f43a03e98bb1d3357c7eb8c263599 Context-only references	Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data Original source ↗ somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion 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.pins` 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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Stable ID: use-case-mapping-somatic-wes-synthetic-20261011-bamsurgeon-wes-snv

field: links:assessed_by:somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv
value: somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv
relevance: proxy
endpoint: Recall and precision of Mutect2, Strelka2 and FreeBayes PASS SNV calls on a BAMSurgeon synthetic WES tumour-normal pair
rationale: Proxy, not direct: the inputs and endpoint match the use case (tumour-normal WES, per-caller precision and recall), but the tumour is synthetic, with SNVs inserted into otherwise clean reads, so precision is near 1 by construction and recall mostly reflects default filtering of inserted low-VAF variants.
constraints: Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; truth sets, specimens, sequencing and caller versions differ between sources.
limitations: One synthetic WES pair; BAMSurgeon inserts SNVs into real reads but does not model tumour artefacts, so almost no false positives are expected (Discussion).; SNVs only; indels not evaluated.; Callers run with nf-core/sarek 3.5.0 defaults and no tuning; no custom panel of normals was specified, and sarek's default GATK GRCh38 panel of normals was applied to Mutect2 (Discussion).; Mutect2 is reported as 'version 2.2', which is not a GATK release number; the GATK version is not stated.; FreeBayes row is internally inconsistent: TP 1,908 plus FN 2,314 is 4,222, not the 4,709 printed as Total Truth, and the printed recall 0.4519 equals 1,908/4,222, whereas 1,908/4,709 is 0.4052. Mutect2 and Strelka2 rows sum to 4,709. The source does not say which value is wrong.; Authors are from the clinical group that generated the patient samples; they did not develop the callers.
citation locators: source id: somatic-wes-synthetic-20261011-source-lopezcade2025; locator: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion
source locator: somatic-wes-synthetic-20261011-source-lopezcade2025: Table 1; Methods 2.3 'Generation of Synthetic Data with Known Somatic SNVs', 2.4 'Variant Calling and Bioinformatic Workflow', 'Performance Evaluation'; Discussion
headline metric: recall
reason: Add a relevance judgement from the 2026-10-11 oncology use-case literature pass.
comparison group: lopezcade2025-wes-synthetic
comparison title: Three callers on a synthetic WES pair (López-Cade et al. 2025)
stratum label: Synthetic WES, SNVs
stratum order: 1
excluded evaluations: id: somatic-wes-synthetic-20261011-eval-freebayes-bamsurgeon-wes-snv; reason: Table 1 row is internally inconsistent: TP plus FN is 4,222, not the 4,709 truth variants, and the printed recall uses 4,222 as denominator.
reviewed evaluations: somatic-wes-synthetic-20261011-eval-mutect2-bamsurgeon-wes-snv; somatic-wes-synthetic-20261011-eval-strelka2-bamsurgeon-wes-snv
review: method: ai-assisted-source-review; scope-review; method note: Reviewer checked the endpoint against the use case's inputs and output, the relevance rating and the limitations; every evaluation on the protocol had its values checked in the batch review. Corrections listed in review.md were applied by the extractor.; reviewer: claude; reviewer note: Claude research agent reviewer-onc-1, independent of the extractor uc-oncology; no human review claimed; reviewed at: 2026-10-11T23:30:00Z; note: Automated review; not human scientific review. See docs/reviews/use-cases/tumour-dna-somatic-variant-detection-2026-10-11.md.
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subject: Select a tumour DNA somatic variant-calling workflow

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