False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) of Mutect2 GATK v4.2.6.1, tumour-only, Illumina (Chen et al. 2025) on COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)
514 False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)
Methods
- Tested configuration
- Mutect2 GATK v4.2.6.1, tumour-only, Illumina (Chen et al. 2025)
- Protocol
- Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b)
- Dataset
- COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)
- Procedure
- Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b)
- Evaluation
- Mutect2 on illumina-colo829 tumour-only Indel (Chen et al. 2025)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN'
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
- Held-out cell line
- Adaptation
- Not reported
- Scoring implementation
- som.py (hap.py 0.3.12) and ClairS-TO compare_vcf; precision, recall and F1 at the best-F1 quality threshold
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 514 Individual claims | ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2025-10-31; PMC12579226 full-text XML | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Parsed the text layer of the pinned Supplementary Information PDF (pdftotext -layout, version 26.08.0) with extract/extract_clairs_to.py; each printed row was matched in order to the authors' Source Data sheet for the same table, whose row labels give the caller, coverage and type, and every printed number was asserted equal to the Source Data value at the printed precision. Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN' 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 514 Individual claims | ClairS-TO Source Data workbook Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Parsed the text layer of the pinned Supplementary Information PDF (pdftotext -layout, version 26.08.0) with extract/extract_clairs_to.py; each printed row was matched in order to the authors' Source Data sheet for the same table, whose row labels give the caller, coverage and type, and every printed number was asserted equal to the Source Data value at the printed precision. Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN' 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 514 Individual claims | ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Parsed the text layer of the pinned Supplementary Information PDF (pdftotext -layout, version 26.08.0) with extract/extract_clairs_to.py; each printed row was matched in order to the authors' Source Data sheet for the same table, whose row labels give the caller, coverage and type, and every printed number was asserted equal to the Source Data value at the printed precision. Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN' 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
- ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling · Original source · Nature Communications, published 2025-10-31; PMC12579226 full-text XML
- ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) · Original source · Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article
- ClairS-TO Source Data workbook · Original source · Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article
Technical metadata and extraction receipts
Stable ID: somatic-clairs-to-20261011-result-mutect2-illumina-colo829-indel-50x-false-negative-count
- metric
- false-negative-count
- metric direction
- lower
- unit
- count
- printed value
- 514
- source locator
- Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN'
- 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: 806cd47423031495bf00543d7e3e3abad3f93fc4ee3ee2a7a570c335227f5603; retrieval url: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-025-64547-z/MediaObjects/41467_2025_64547_MOESM1_ESM.pdf; note: Extraction: Parsed the text layer of the pinned Supplementary Information PDF (pdftotext -layout, version 26.08.0) with extract/extract_clairs_to.py; each printed row was matched in order to the authors' Source Data sheet for the same table, whose row labels give the caller, coverage and type, and every printed number was asserted equal to the Source Data value at the printed precision. Supplementary Table 7b, Dataset 'COLO829', Caller 'Mutect2', Tumor coverage '50x', Type 'Indel', column 'FN' 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
- 514
- metric qualifier
- indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold
- unit detail
- counted entity: truth variants not called
- missing metadata
- uncertainty: reason: unreported