0.509 precision
guille2025-strelka-seqc2-fd-wes-snv precision (snv only)
- Tested configuration
- Strelka 2.9.2 (Guille et al. 2025)
- Protocol
- SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)
- Dataset
- SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions
- Procedure
- somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv
- Evaluation
- Strelka on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedA benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I10; Tools 'Strelka'; column 'PPV'
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 validation sample
- Adaptation
- Not reported
- Scoring implementation
- Not reported
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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.509462915601023 Individual claims | A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I10; Tools 'Strelka'; column 'PPV' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit detailsExtracted by deterministic parse of the pinned legacy XLS (BIFF8) workbook with a standard-library reader (extract/rawxls.py, called by extract/extract_somatic.py), with the title, column headers, row labels, vote counts, categories and variant types asserted. printed_value is the shortest round-trip decimal of the stored double; raw_xml_value keeps that stored value as text (the file is BIFF, not XML). Spreadsheet display formatting was not applied. Pending independent review. Independent review 2026-10-09: value and identity match the source; TPR, PPV and F1 recompute exactly from TP, FP and P. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 0.509462915601023 Individual claims | Guille et al. 2025, Supplementary Table S7 (validation dataset) Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I10; Tools 'Strelka'; column 'PPV' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: tables7_bbae697.xls inside the Europe PMC supplementary files bundle for PMC11790059 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit detailsExtracted by deterministic parse of the pinned legacy XLS (BIFF8) workbook with a standard-library reader (extract/rawxls.py, called by extract/extract_somatic.py), with the title, column headers, row labels, vote counts, categories and variant types asserted. printed_value is the shortest round-trip decimal of the stored double; raw_xml_value keeps that stored value as text (the file is BIFF, not XML). Spreadsheet display formatting was not applied. Pending independent review. Independent review 2026-10-09: value and identity match the source; TPR, PPV and F1 recompute exactly from TP, FP and P. Field: Source artifact SHA-256: Hash scope: SHA-256 of tables7_bbae697.xls. Retrieved as one member of the Europe PMC supplementaryFiles zip. The zip is assembled per request (member timestamps equal the request time), so only the member file hash is pinned. Archive member: tables7_bbae697.xls Extraction artifact SHA-256: |
Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
2 source records and release history
- A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing · Original source · Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML
- Guille et al. 2025, Supplementary Table S7 (validation dataset) · Original source · tables7_bbae697.xls inside the Europe PMC supplementary files bundle for PMC11790059
Technical metadata and extraction receipts
Stable ID: somatic-20261009-result-guille2025-strelka-seqc2-fd-wes-snv-precision
- metric
- precision
- metric direction
- higher
- unit
- fraction
- metric qualifier
- snv only
- printed value
- 0.509462915601023
- numeric value
- 0.509462915601023
- raw xml value
- 0.509462915601023
- source locator
- Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I10; Tools 'Strelka'; column 'PPV'
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the Europe PMC supplementary zip; the tables7_bbae697.xls member matched its SHA-256. Read the cell with a separate stdlib BIFF8 reader written for this review; the extractor's rawxls.py was not imported or run. Checked printed and numeric value, metric, qualifier, unit and direction from the column header, row label and variant type, the linked evaluation's configuration and protocol, and the truth count P. TPR, PPV and F1 were recomputed from TP, FP and P.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: 735470fcb1ae7c3578ab3efefe12fde4b73bac279a1e7185950e5c2c0f1073f2; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11790059/supplementaryFiles; note: Extracted by deterministic parse of the pinned legacy XLS (BIFF8) workbook with a standard-library reader (extract/rawxls.py, called by extract/extract_somatic.py), with the title, column headers, row labels, vote counts, categories and variant types asserted. printed_value is the shortest round-trip decimal of the stored double; raw_xml_value keeps that stored value as text (the file is BIFF, not XML). Spreadsheet display formatting was not applied. Pending independent review. Independent review 2026-10-09: value and identity match the source; TPR, PPV and F1 recompute exactly from TP, FP and P.