Result

0.769 recall

Evidence concern: excluded from comparisons

Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999

Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement

nardone2025-manta recall (deletions, over 20000 bp)

Tested configuration: Manta v1.6.0 (Nardone et al.)
Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1)
Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)
Procedure: cnv-20261009-protocol-nardone2025-hg002-del-wittyer
Evaluation: Manta on HG002 deletions (Nardone et al.)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedA Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H43; Method Manta; Interval >20000; 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 HG002 sample
Adaptation: Not reported
Scoring implementation: Witty.er v0.5.2 (Methods 2.4); matching parameters unreported

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 0.7692 Individual claims	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ TableS1.xlsx, H43; Method Manta; Interval >20000; column Recall Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Biomedicines 13(8):1949, published 2025-08-09; PMC12383524 full-text XML Retrieved: 2026-10-09T15:28:17Z	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: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14` Extraction artifact
Reported result 0.7692 Individual claims	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ TableS1.xlsx, H43; Method Manta; Interval >20000; column Recall Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: TableS1.xlsx inside biomedicines-13-01949-s001.zip Retrieved: 2026-10-09T15:28:17Z	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: `1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 86c46fdc3e9125ae8e025ac4d1c9129dd4631039abd56019581e242dc3ae3d70; biomedicines-13-01949-s001.zip 678880a4c36070dfaf0813421d82a4e2747a85cb5a85c8c886b321a58be8ecf9. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact Extraction artifact SHA-256: `1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14` Extraction artifact

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Sources and history

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

2 source records and release history

A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Original source · Biomedicines 13(8):1949, published 2025-08-09; PMC12383524 full-text XML
Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Original source · TableS1.xlsx inside biomedicines-13-01949-s001.zip

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Technical metadata and extraction receipts

Stable ID: cnv-20261009-result-nardone2025-manta-recall-gt20000

metric: recall
metric qualifier: deletions, over 20000 bp
metric direction: higher
unit: fraction
printed value: 0.7692
numeric value: 0.7692
source locator: TableS1.xlsx, H43; Method Manta; Interval >20000; 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 (Nardone TableS1.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 and FN cells of the same row.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: 1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12383524/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: 10; fp: 18; fn: 3
raw xml value: 0.76919999999999999

Related records

evaluation: Manta on HG002 deletions (Nardone et al.)

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