Accelerated long-read variant calling with Clair3: Supplementary Data
btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 · Peer-reviewed
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Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Claims
Statements this source supports, each with where in the source it was checked.
- Relevance of Clair3 GPU workflow stage runtimes on HG003 ONT and PacBio WGS (Zheng et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics": Assessed by Clair3 GPU workflow stage runtimes on HG003 ONT and PacBio WGS (Zheng et al. 2026 Supplementary Table 1) (model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 1; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability)
- Relevance of HG003 ONT 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": Assessed by HG003 ONT WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3) (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)
- Relevance of HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics": Assessed by HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) (model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 2; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability)
- 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": Assessed by HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3) (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)
- Relevance of HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026) to "Select an execution workflow for large-scale diagnostic genomics": Assessed by HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2) (model-execution-20261011-source-zheng2026-clair3-supplement: Supplementary Table 2; Supplementary Notes; model-execution-20261011-source-zheng2026-clair3: Results 3.1-3.2; Conflict of interests; Data availability)
- version: DeepVariant runs (Zheng et al. 2026): Version Supplementary Table 2 and the Supplementary Notes command lines give DeepVariant v1.10-beta (google/deepvariant:v1.10-beta and v1.10-beta-gpu); Results 3.1 compare 'DeepVariant v1.8 in CPU and GPU modes'. Supplementary Table 3 prints no version. (Supplementary Table 2 caller column; Supplementary Notes 'Running DeepVariant GPU version (v1.10-beta)' and 'Running DeepVariant CPU (v1.10-beta)'; Results 3.1.1 paragraph 1)
Models, benchmarks and other records
Configurations (5)
Protocols (5)
- Clair3 GPU workflow stage runtimes on HG003 ONT and PacBio WGS (Zheng et al. 2026 Supplementary Table 1)
- HG003 ONT WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
- HG003 ONT WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2)
- HG003 PacBio Revio WGS small-variant accuracy against GIAB v4.2.1, Clair3 versus DeepVariant (Zheng et al. 2026 Supplementary Table 3)
- HG003 PacBio Revio WGS variant-calling runtime, memory and I/O, Clair3 versus DeepVariant in GPU mode (Zheng et al. 2026 Supplementary Table 2)
Datasets (2)
Evaluations (12)
- Clair3 pileup, HG003 ONT small-variant accuracy (Zheng et al. 2026)
- Clair3 pileup, HG003 PacBio small-variant accuracy (Zheng et al. 2026)
- Clair3 v1.2.0 (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026)
- Clair3 v1.2.0 (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026)
- Clair3 v1.2.0 GPU stage runtimes, HG003 ONT (Zheng et al. 2026)
- Clair3 v1.2.0 GPU stage runtimes, HG003 PacBio (Zheng et al. 2026)
- Clair3, HG003 ONT small-variant accuracy (Zheng et al. 2026)
- Clair3, HG003 PacBio small-variant accuracy (Zheng et al. 2026)
- DeepVariant v1.10-beta (GPU mode), HG003 ONT runtime and memory (Zheng et al. 2026)
- DeepVariant v1.10-beta (GPU mode), HG003 PacBio runtime and memory (Zheng et al. 2026)
- DeepVariant, HG003 ONT small-variant accuracy (Zheng et al. 2026)
- DeepVariant, HG003 PacBio small-variant accuracy (Zheng et al. 2026)
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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Artifact member btag181_supplementary_data.pdf Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
| attributes.artifact_sha256 feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9 Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
| Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13141153/supplementaryFiles Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
| Doi 10.1093/bioinformatics/btag181 Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
Evidence concerns1 values
| Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
| Licence CC-BY-4.0 Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
| Media type application/pdf Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
| Publication status peer_reviewed Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
| Retrieval note Europe PMC supplementaryFiles zip (SHA-256 b0df24a11fb7652c6d0f6f359c6f02ed2de092ea820e93c2c2841645aa2cf3c6); artifact_sha256 is the PDF member. Supplementary Tables 2 and 3 are raster images in the PDF with no text layer. Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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 |
| Retrieved at 2026-10-11T21:42:40Z Source metadata | Accelerated long-read variant calling with Clair3: Supplementary Data No field-specific location recorded Version: btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153 | catalogued 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
Supplementary PDF retrieved and hashed for the diagnostic genomics execution literature pass (2026-10-11).
Technical metadata and extraction receipts
Stable ID: model-execution-20261011-source-zheng2026-clair3-supplement
- areas
- dna-genomes
- contexts
- research
- url
- https://doi.org/10.1093/bioinformatics/btag181
- artifact url
- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13141153/supplementaryFiles
- version
- btag181_supplementary_data.pdf from the Europe PMC supplementary files of PMC13141153
- retrieved at
- 2026-10-11T21:42:40Z
- artifact sha256
- feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9
- doi
- 10.1093/bioinformatics/btag181
- publication status
- peer_reviewed
- licence
- CC-BY-4.0
- media type
- application/pdf
- artifact member
- btag181_supplementary_data.pdf
- evidence concerns
- source id: model-execution-20261011-source-zheng2026-clair3-supplement; message: Supplementary Table 2 runtimes differ from the article's Results for what appear to be the same HG003 comparisons. ONT at 30x and 50x: Clair3 GPU 17 and 20 minutes in the table, 16 and 15 in Results 3.1.1; DeepVariant GPU 48 and 82 in the table, 106 to 128 in the text. PacBio Revio at 30x and 50x: Clair3 GPU 12 and 12 in the table, 23 and 21 in Results 3.1.2; DeepVariant GPU 40 and 53 in the table, 93 and 118 in the text. The table's Clair3 PacBio runtimes equal the macOS M3 Ultra runtime in Results 3.1.3, not the Linux RTX 4090 runtimes. The table and the Supplementary Notes commands give DeepVariant v1.10-beta; Results 3.1 say v1.8. Supplementary Table 3 DeepVariant ONT SNP precision, recall and F1 at 10x and 20x (97.58%, 92.35%, 94.89% and 99.32%, 99.02%, 99.17%) differ from Results 3.2 (97.34%, 92.17%, 94.68% and 98.75%, 98.79%, 98.79%), while the Clair3 values agree. Results 3.2 cite Supplementary Table 2 for the HG001 to HG007 comparison, which is Supplementary Table 4. The hardware, DeepVariant version and runs behind Supplementary Tables 2 and 3 are therefore uncertain. Supplementary Table 1 agrees with Results 3.1.4 except WhatsHap ONT 30x (723 seconds in the table, 724 in the text). Table values are recorded; text values are not.; source locator: Supplementary Tables 1 to 3 (pages 2 and 3) versus article Results 3.1.1 to 3.1.4 and 3.2; artifact sha256: feec482c5befbb44f93b82782b200a3abebaf7d81a0aad81e28de191be1523d9; reviewed at: 2026-10-12T07:50:32Z; review method: automated-source-review
- retrieval note
- Europe PMC supplementaryFiles zip (SHA-256 b0df24a11fb7652c6d0f6f359c6f02ed2de092ea820e93c2c2841645aa2cf3c6); artifact_sha256 is the PDF member. Supplementary Tables 2 and 3 are raster images in the PDF with no text layer.