Result

0.434 recall

gabrielaite2021-cnvnator-na12878-wgs recall (na12878 wgs, 1 bp overlap)

Tested configuration: CNVnator (Gabrielaite et al. WGS)
Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2)
Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set
Procedure: cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap
Evaluation: CNVnator on NA12878 WGS
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedA Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L136; sample GB-WGS-NA12878; tool CNVnator; column recall

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 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 0.434489402697495 Individual claims	A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Original source ↗ Table S2.xlsx, sheet Supplementary_table2, L136; sample GB-WGS-NA12878; tool CNVnator; column recall Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Cancers 13(24):6283, published 2021-12-14; PMC8699073 full-text XML Retrieved: 2026-10-09T15:21:28Z	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: `d8e954e141a06601b11b986338e45b57a3d5a98ac9e85411895b0ca1249b790f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `eb4bb389b248508531ca371ba80e004a573f4e85029583cff336f217307fde85` Extraction artifact
Reported result 0.434489402697495 Individual claims	Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Original source ↗ Table S2.xlsx, sheet Supplementary_table2, L136; sample GB-WGS-NA12878; tool CNVnator; column recall Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip Retrieved: 2026-10-09T15:21:28Z	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: `eb4bb389b248508531ca371ba80e004a573f4e85029583cff336f217307fde85` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact Extraction artifact SHA-256: `eb4bb389b248508531ca371ba80e004a573f4e85029583cff336f217307fde85` Extraction artifact

All evidence (JSONL) (gzip)How to read the evidence

Sources and history

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

2 source records and release history

A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data · Original source · Cancers 13(24):6283, published 2021-12-14; PMC8699073 full-text XML
Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Original source · Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: cnv-20261009-result-gabrielaite2021-cnvnator-na12878-wgs-recall

metric: recall
metric qualifier: na12878 wgs, 1 bp overlap
metric direction: higher
unit: fraction
printed value: 0.434489402697495
numeric value: 0.434489402697495
source locator: Table S2.xlsx, sheet Supplementary_table2, L136; sample GB-WGS-NA12878; tool CNVnator; column recall
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 (Gabrielaite Table S2.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. Checked scoring_conditions against the TP, FP, FN, N_truth, N_DEL and N_DUP cells and recomputed the value from TP, FP and FN.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: eb4bb389b248508531ca371ba80e004a573f4e85029583cff336f217307fde85; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8699073/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.
scoring conditions: tp: 902; fp: 6168; fn: 1174; n truth: 2076; n called del: 6830; n called dup: 240; denominator formula: TP+FN
raw xml value: 0.43448940269749498

Related records

evaluation: CNVnator on NA12878 WGS

Suggest a correction