AUPRC (SNV only, tumour-only) of Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026) on SEQC2 HCC1395 tumour Illumina HiSeq WGS (WGS_IL_T_1), high-confidence regions
0.078 AUPRC (SNV only, tumour-only)
Methods
- Tested configuration
- Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)
- Protocol
- SEQC2 HCC1395 tumour-only, SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1)
- Dataset
- SEQC2 HCC1395 tumour Illumina HiSeq WGS (WGS_IL_T_1), high-confidence regions
- Procedure
- SEQC2 HCC1395 tumour-only, SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1)
- Evaluation
- Mutect2 (tumor-only) on seqc2-snv tumour-only (Krishnamachari et al. 2026)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedImproved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV'
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
- Not in VarNet-T training
- Adaptation
- Not reported
- Scoring implementation
- AUPRC over the caller's own score
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.078 Individual claims | Improved tumor-only variant calling and mutation burden estimation with VarNet-T Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 full-text XML | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Parsed from the text layer of the pinned Supplementary Information PDF (physical pages 18 and 21; pdftotext -layout, version 26.08.0) with extract/extract_varnet_t.py; method labels asserted, every cell cross-checked against the authors' Source Data sheet of the same name, and the Results values 0.773, 0.577 and 0.656 checked. Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV' 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 0.078 Individual claims | VarNet-T Source Data workbook Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2026_71705_MOESM6_ESM.xlsx) | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Parsed from the text layer of the pinned Supplementary Information PDF (physical pages 18 and 21; pdftotext -layout, version 26.08.0) with extract/extract_varnet_t.py; method labels asserted, every cell cross-checked against the authors' Source Data sheet of the same name, and the Results values 0.773, 0.577 and 0.656 checked. Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV' 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 0.078 Individual claims | VarNet-T Supplementary Information Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Parsed from the text layer of the pinned Supplementary Information PDF (physical pages 18 and 21; pdftotext -layout, version 26.08.0) with extract/extract_varnet_t.py; method labels asserted, every cell cross-checked against the authors' Source Data sheet of the same name, and the Results values 0.773, 0.577 and 0.656 checked. Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV' 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- Improved tumor-only variant calling and mutation burden estimation with VarNet-T · Original source · Nature Communications, published 2026-04-09; PMC13243554 full-text XML
- VarNet-T Supplementary Information · Original source · Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages
- VarNet-T Source Data workbook · Original source · Source Data file (41467_2026_71705_MOESM6_ESM.xlsx)
Technical metadata and extraction receipts
Stable ID: somatic-varnet-t-20261011-result-mutect2-tumor-only-seqc2-snv-auprc
- metric
- auprc
- metric direction
- higher
- unit
- fraction
- printed value
- 0.078
- source locator
- Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV'
- review
- method: source-hash-verification; pdf-text-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: c808b4361e17a64911a59ded81d9db04c7a3dd5ba95fb3e1e060a293182f2842; retrieval url: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-026-71705-4/MediaObjects/41467_2026_71705_MOESM1_ESM.pdf; note: Extraction: Parsed from the text layer of the pinned Supplementary Information PDF (physical pages 18 and 21; pdftotext -layout, version 26.08.0) with extract/extract_varnet_t.py; method labels asserted, every cell cross-checked against the authors' Source Data sheet of the same name, and the Results values 0.773, 0.577 and 0.656 checked. Supplementary Table 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV' 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
- 0.078
- metric qualifier
- SNV only, tumour-only
- missing metadata
- uncertainty: reason: unreported