Result

0.889 recall

delavega2025-delly recall (deletions, 10-50 kb)

Tested configuration: DELLY (De La Vega et al.)
Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3)
Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models
Procedure: cnv-20261009-protocol-delavega2025-hg002-exon-overlap
Evaluation: Delly (v1.1.6) on HG002 exon-overlap benchmark
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedBenchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, J11; row 'Delly (v1.1.6)'; group 'deletions, 10-50 kb'; column Sensitivity

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: Single HG002 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

Claims, original sources and review scope · Release 2026-10-09-9307685239b3
Property and statement	Original source and location	Review and provenance
Reported result 0.8889 Individual claims	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Supplemental Table 3, J11; row 'Delly (v1.1.6)'; group 'deletions, 10-50 kb'; column Sensitivity Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Extracted by deterministic parse of the pinned XLSX cell XML (scripts in the batch retrieval log), with row and column labels asserted. printed_value is the shortest round-trip decimal of the stored cell value; source_cell_text keeps the raw stored text. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde` Extraction artifact
Reported result 0.8889 Individual claims	De La Vega et al. 2025, Supplemental Table 3 Original source ↗ Supplemental Table 3, J11; row 'Delly (v1.1.6)'; group 'deletions, 10-50 kb'; column Sensitivity Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip Retrieved: 2026-10-09T15:24:22Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit details Extracted by deterministic parse of the pinned XLSX cell XML (scripts in the batch retrieval log), with row and column labels asserted. printed_value is the shortest round-trip decimal of the stored cell value; source_cell_text keeps the raw stored text. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 52ad070b6703eb204924cb099e6bcbcdce0a4946235d3ef1c7c290469017584f; vbaf071_supplementary_data.zip 82318e5f18b797a277241a1b206a9aadd1e856cf4293eb79729185d314029691. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact Extraction artifact SHA-256: `d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde` Extraction artifact

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Sources and history

Release 2026-10-09-9307685239b3 · Record review: source checked

2 source records and release history

Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Original source · Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML
De La Vega et al. 2025, Supplemental Table 3 · Original source · Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: cnv-20261009-result-delavega2025-delly-recall-j

metric: recall
metric qualifier: deletions, 10-50 kb
metric direction: higher
unit: fraction
printed value: 0.8889
numeric value: 0.8889
source locator: Supplemental Table 3, J11; row 'Delly (v1.1.6)'; group 'deletions, 10-50 kb'; column Sensitivity
missing metadata: uncertainty: reason: unreported
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the artifact and matched its SHA-256. Read the cell with a separate stdlib OOXML/XML parser written for this review (De La Vega Supplemental_Table_3.xlsx); the extractor's scripts were not imported or run. Checked printed and numeric value (shortest round-trip decimal of the stored double), raw cell text, metric, qualifier, unit and direction from the row and column headers, and the linked evaluation's configuration and protocol.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12005901/supplementaryFiles; note: Extracted by deterministic parse of the pinned XLSX cell XML (scripts in the batch retrieval log), with row and column labels asserted. printed_value is the shortest round-trip decimal of the stored cell value; source_cell_text keeps the raw stored text. Pending independent review. Independent review 2026-10-09: value and identity match the source.
raw xml value: 0.88890000000000002

Related records

evaluation: Delly (v1.1.6) on HG002 exon-overlap benchmark

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