rewirebio.iobenchmarks

Use caseDNA and genomesResearch and clinical research

Select a copy-number variant detection and characterisation workflow

Which workflow detects and characterises copy-number changes accurately and helps an analyst assess the evidence?

In this release 1 evaluated endpoint · 1 tested configuration · Direct evidence for the stated endpoint · 3 recorded evidence gaps

Question and applicability

Inspect the DRAGEN 4.2 CNV/SV benchmarking F-score evidence for 1-5 kb deletions before selecting a workflow; evidence-visualisation usability is not addressed by this bounded intake.

Who this is for
  • Clinical researchers scoping the available diagnostic-genomics evidence
  • Computational researchers comparing exact evaluated configurations
Research setting

Research and clinical research. See Clinical research scope for what the evidence does not establish.

Biological setting
DRAGEN 4.2's CNV/SV benchmarking (HG002, GIAB SV truth set) reports an F-score for 1-5 kb deletion detection (selected Table S4 cells, sheet CNVbenchmarking, H6=.926, L6=.391).

Outside this use case

  • Duplications, larger/smaller size strata, and tumour CNV (not ingested in this bounded intake)
  • Evidence-visualisation usability for an analyst (not measured by this F-score endpoint)

Inputs and expected output

Inputs you need

  • Whole-genome sequencing aligned reads
  • The size range and variant class (deletion, duplication, etc.) of clinical interest

Expected output

A sourced F-score for one size-stratified deletion class against a truth set; no visualisation-usability or clinical-reporting claim.

Clinical research scope

Clinical applicability is not established beyond this one size-stratified deletion F-score; a conflicting comparator figure (.391 vs 39.20% in source table/prose) is preserved unresolved and not promoted.

Evaluated evidence

Evidence is grouped by its protocol. Relevance refers to the stated endpoint and context; it is separate from clinical validation and from the review method. Limits specific to each evaluation are listed with it.

HG002 GIAB v0.6 CNV deletion 1–5kb F-score

Current source-reviewed mapping

Direct evidence for the stated endpoint

F-score for 1-5 kb deletion detection against a GIAB truth set directly measures the declared CNV-detection endpoint; it does not cover visualisation usability.

Assessed endpoint
F-score for 1-5 kb deletion detection (DRAGEN 4.2 CNV/SV benchmarking, HG002) against the GIAB SV truth set
Evaluation protocol
HG002 GIAB v0.6 CNV deletion 1–5kb F-score
Computational task
A reviewed task relationship is not recorded for this protocol.
Input and population constraints
  • Inspect every linked evaluation's source locator and preserved conflicts before citing a result.
  • Do not combine this mapping's evaluations with any other protocol's results.

Limits on interpretation

  • Unreported per-bin counts
  • No duplication/tumourCNV/clinical endpoint
  • No visualisation usability
  • CNVnator table/prose conflict
  • No foundation-model applicability

Automated source review · 2026-10-07 · Claude Sonnet AMP-integration worker, bounded transcription of Codex-checked primary values; independently reviewed by Codex (workbench/amp-supervision/primary-review.md, integration-review-corrections.md)

Bounded primary-source transcription, independently Codex-checked. No new model execution, independent experimental reproduction, qualified human scientific review or clinical validation.

Evaluated configurations

Each configuration below belongs to this protocol. Inspect its inputs, population and scoring conditions before comparing it with another evaluation.

DRAGEN 4.2 CNV+SV configuration

Author-reported evaluation · Source checked

Scoped author-reported evidence candidate; no clinical recommendation.

Inspect results, conditions and reproduction (1 recorded result)
Population and split
SingleHG002; [1000,5000)bp truth deletions, exact count unreported · Single HG002 benchmark sample
Inputs and adaptation
35× WGS; GRCh37 GIAB v0.6 deletion truth · Not reported
Evaluation budget
Not reported
Runtime and memory

Runtime and memory measurements are not reported in this evaluation. A study budget is not a runtime or memory measurement.

Recorded results for this configuration
MetricValueCoverageUncertainty and source
F-score0.926

fraction · higher

Not reported scored / Not reported eligible

Not reported

Result provenance

Uncertainty: Unreported

Evaluation methods, evidence and reproduction

No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.

Open the protocol's results and comparison checks →

Mapping sources and review metadata

Mapping use-case-mapping-amp-20261007-issue17 · revision 1

Add Codex-checked primary-source protocol evidence from the bounded AMP intake (rewire.it#365).

Reviewed evidence fingerprint 98e91a04803fe81a2302567c8942d3ec69a99c86179c781c6f06b5f9ba0a476e

Limitations and missing evidence

These gaps apply to the question as a whole. Absence of evidence is not a zero score.

  • Unreported per-bin counts behind the printed F-score.
  • No duplication, tumour-CNV or clinical-reporting endpoint is ingested in this bounded intake.
  • No foundation-model applicability is established for this task.

Planned work

These plans do not contribute measured results or evaluated winners above.

Contribute evidence or propose a correction

Evidence collection plan

Collecting evidence

Mapped evidence already covers 1 evaluated endpoint, in the evaluated evidence above. The status above describes only the specific comparison in this plan, which remains open; it does not mean no evidence has been collected. The plan defines a comparison to investigate; it does not establish model performance or suitability.

Comparison question

Which workflow detects and characterises copy-number changes accurately and helps an analyst assess the evidence?

Baselines, outcomes and validation requirements

Baselines to include

  • The conventional/author-introduced workflow measured in the linked primary source(s).

Outcomes to measure

  • The declared endpoint in this use case's active mapping(s); see evidence_gaps for what remains open.

Validation requirements

  • Independent held-out population matched to the intended clinical setting.
  • Qualified human scientific review before any clinical-validation claim.

Next collection task

A dedicated rewire-benchmarks protocol/run task covering duplications and tumour CNV, plus an analyst-facing visualisation-usability evaluation.

Sources and review

Automated source review · 2026-10-07 · Claude Sonnet AMP-integration worker, bounded transcription of Codex-checked primary values; independently reviewed by Codex (workbench/amp-supervision/primary-review.md, integration-review-corrections.md)

Bounded primary-source transcription, independently Codex-checked. No new model execution, independent experimental reproduction, qualified human scientific review or clinical validation.

Release provenance and downloads

Release 2026-10-07-1448159e6a81

Use-case input digest d60fd7f669bfec7bd34ec6e5080d8e1cb4e8186f8286ead60888848f1e20e001

Download questions, collection plans and review metadata (JSON) · Verify release checksums

Question use-case-cnv-detection-characterisation. Any numerical results on this page come from this release's existing evaluation records.