Relevance of HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics"
- Use case
- Select an execution workflow for large-scale diagnostic genomics
- Assessed by
- HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
- Relevance
- Proxy evidence
- Endpoint
- Precision, recall and F1 for SNPs, indels and both against GIAB v4.2.1 HG003 for Clair3, Clair3 pileup-only and DeepVariant on PacBio Revio WGS at 10x to 50x
Accuracy for the PacBio Revio runs of the same sample and coverages as the runtime table. Proxy for the same reasons as the ONT accuracy protocol.
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.
40 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations2 values
| Accelerated long-read variant calling with Clair3 for whole-genome sequencing model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations2 values
| Accelerated long-read variant calling with Clair3: Supplementary Data model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf |
| Comparison group zheng2026-hg003-accuracy Context-only references | Accelerated long-read variant calling with Clair3 for whole-genome sequencing model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group zheng2026-hg003-accuracy Context-only references | Accelerated long-read variant calling with Clair3: Supplementary Data model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf |
| Comparison title Clair3 versus DeepVariant small-variant accuracy on HG003 (Zheng et al. 2026) Context-only references | Accelerated long-read variant calling with Clair3 for whole-genome sequencing model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title Clair3 versus DeepVariant small-variant accuracy on HG003 (Zheng et al. 2026) Context-only references | Accelerated long-read variant calling with Clair3: Supplementary Data model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf |
Constraints2 values
| Accelerated long-read variant calling with Clair3 for whole-genome sequencing model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| Accelerated long-read variant calling with Clair3: Supplementary Data model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf |
| Endpoint Precision, recall and F1 for SNPs, indels and both against GIAB v4.2.1 HG003 for Clair3, Clair3 pileup-only and DeepVariant on PacBio Revio WGS at 10x to 50x Context-only references | Accelerated long-read variant calling with Clair3 for whole-genome sequencing model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Precision, recall and F1 for SNPs, indels and both against GIAB v4.2.1 HG003 for Clair3, Clair3 pileup-only and DeepVariant on PacBio Revio WGS at 10x to 50x Context-only references | Accelerated long-read variant calling with Clair3: Supplementary Data model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: btag181_supplementary_data.pdf |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Accelerated long-read variant calling with Clair3 for whole-genome sequencing · Original source · Bioinformatics 42(5), published 2026-04-10; PMC13141153 full-text XML
- Accelerated long-read variant calling with Clair3: Supplementary Data · Original source · btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153
Technical metadata and extraction receipts
Stable ID: use-case-mapping-model-execution-20261011-zheng2026-hg003-accuracy-pacbio
- field
- links:assessed_by:model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio
- value
- model-execution-20261011-protocol-zheng2026-hg003-accuracy-pacbio
- relevance
- proxy
- endpoint
- Precision, recall and F1 for SNPs, indels and both against GIAB v4.2.1 HG003 for Clair3, Clair3 pileup-only and DeepVariant on PacBio Revio WGS at 10x to 50x
- rationale
- Accuracy for the PacBio Revio runs of the same sample and coverages as the runtime table. Proxy for the same reasons as the ONT accuracy protocol.
- 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; hardware, inputs, software versions and timing boundaries differ between sources.
- limitations
- One value per configuration and coverage is printed; the number of runs behind it is not stated and no spread is printed.; Author-reported: the authors develop Clair3; DeepVariant was run by them.; Results 3.2 quote PacBio 10x values (Clair3 SNP F1 98.54%, indel 91.39%; DeepVariant 97.81% and 90.74%); the DeepVariant 10x values differ slightly from Supplementary Table 3 (97.80% and 91.08%).; No runtime is printed in this table.; The source has an unresolved evidence concern (Supplementary Tables 2 and 3 conflict with the Results text); see the source record.
- revision
- 1
- reason
- Add primary-source execution evidence from the diagnostic genomics execution literature pass (2026-10-11).
- citation locators
- source id: model-execution-20261011-source-zheng2026-clair3-supplement; locator: Supplementary Table 3; Supplementary Notes; source id: model-execution-20261011-source-zheng2026-clair3; locator: Results 3.1-3.2; Conflict of interests; Data availability
- source locator
- model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 3; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability
- comparison group
- zheng2026-hg003-accuracy
- comparison title
- Clair3 versus DeepVariant small-variant accuracy on HG003 (Zheng et al. 2026)
- headline metric
- f1-score
- stratum label
- PacBio Revio
- stratum order
- 2
- review
- method: source-hash-verification; independent-cell-check; scope-review; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent uc-execution extracted and drafted; Claude (Opus 5.5) review agent reviewer-exec checked every value and this judgement against the pinned sources; reviewed at: 2026-10-12T07:50:32Z; note: Bounded primary-source transcription with independent cell check and relevance review. No execution, reproduction, qualified human scientific review or clinical validation.
- reviewed evaluations
- model-execution-20261011-eval-zheng2026-clair3-accuracy-hg003-accuracy-pacbio; model-execution-20261011-eval-zheng2026-clair3-pileup-accuracy-hg003-accuracy-pacbio; model-execution-20261011-eval-zheng2026-deepvariant-accuracy-hg003-accuracy-pacbio
- pins
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