Baseline: Select a copy-number variant detection and characterisation workflow
Baseline of Select a copy-number variant detection and characterisation workflow
ExomeDepth, CNVnator, AnnotSV and ClassifyCNV
Baseline method for the use case, reviewed against its cited sources.
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.
27 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field baseline Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field baseline Context-only references | Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genes 17(1):105, published 2026-01-19; PMC12841491 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field baseline Context-only references | Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids4 values
| A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids4 values
| Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genes 17(1):105, published 2026-01-19; PMC12841491 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids4 values
| Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records4 values
| A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records4 values
| Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genes 17(1):105, published 2026-01-19; PMC12841491 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records4 values
| Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale ExomeDepth (exome) and CNVnator (genome) are read-depth callers that fit statistical models of coverage and are measured in most of the linked detection benchmarks, though no benchmark names one standard caller. AnnotSV and ClassifyCNV apply the ACMG CNV scoring rules, the rule-based reference that machine-learning classifiers are compared with in Zhang et al. 2026. Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories) 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
3 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
- Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Original source · Genes 17(1):105, published 2026-01-19; PMC12841491 full-text XML
- Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) · Original source · Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Technical metadata and extraction receipts
Stable ID: use-case-baseline-cnv-detection-characterisation
- field
- baseline
- value
- ExomeDepth, CNVnator, AnnotSV and ClassifyCNV
- source locator
- cnv-20261009-source-gabrielaite2021: Abstract and Results (callers compared and recommended); cnv-20261011-hwang2026-source-article: Abstract and Materials and Methods 2.3 (ExomeDepth among four WES callers); cnv-20261011-zhang2026-source-article: Methods (rule-based and machine-learning tool categories)
- method ids
- rare-reanalysis-20261009-method-exomedepth; cnv-20261009-method-cnvnator; cnv-20261011-zhang2026-method-annotsv; cnv-20261011-zhang2026-method-classifycnv
- rationale
- ExomeDepth (exome) and CNVnator (genome) are read-depth callers that fit statistical models of coverage and are measured in most of the linked detection benchmarks, though no benchmark names one standard caller. AnnotSV and ClassifyCNV apply the ACMG CNV scoring rules, the rule-based reference that machine-learning classifiers are compared with in Zhang et al. 2026.
- review
- method: source-hash-verification; automated-source-review; reviewer: claude; reviewer note: Separate Claude review agent, independent of the agent that proposed the baseline; no human review claimed; reviewed at: 2026-10-12T18:00:00Z; note: Reviewer corrected rationale and source list. Sources re-retrieved and read; method records and their configuration links checked against the use case's active comparisons. Names the reference newer methods are compared with, not a recommendation. See docs/reviews/use-cases/baselines-2026-10-12.md.
- pins
- record id: cnv-20261009-source-gabrielaite2021; fields: status; attributes.artifact_sha256; sha256: be33c599db24d24638e904513ed51c917eaac09eda645463a113d37012121328; record id: cnv-20261011-hwang2026-source-article; fields: status; attributes.artifact_sha256; sha256: 33f5227b8d66ed68dc50ac7f888035552a9445a6ed4d118017989976041478d5; record id: cnv-20261011-zhang2026-source-article; fields: status; attributes.artifact_sha256; sha256: 0e820fd41bddc8e50da7eda300178b6975ae8e3a43214db18cabd9fe1ab836a6; record id: use-case-cnv-detection-characterisation; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: e86232bbdd2e9f2de3ba90f86e72b53bdd8368f9c0ddc74b7ee5870155f0a0d0