Configuration

CNVkit v0.9.7, post-filter (Hwang et al. 2026)

CNVkit on clinical exomes with the authors' problematic-region filter.

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Evaluations and results

1 evaluation · 6 results. Different protocols are not a single leaderboard.

Protocol: Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-filter) · Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)

Sorted by False negatives (exon level) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	False negatives (exon level)	False positives (exon level)	Precision (exon level)	Recall (exon level)	True positives (exon level)	Count (exon level; reference CMA CNV exons in the evaluated set)
CNVkit v0.9.7, post-filter (Hwang et al. 2026)Evaluation	866	6578	0.219	0.68	1844	2710

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CNVkit v0.9.7, post-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	866 False negatives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNVkit (post-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-post-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FN', column 'CNVkit' / 'Post-filter'
Configuration: CNVkit v0.9.7, post-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	6580 False positives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNVkit (post-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-post-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FP', column 'CNVkit' / 'Post-filter'
Configuration: CNVkit v0.9.7, post-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.219 Precision (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNVkit (post-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-post-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'PPV', column 'CNVkit' / 'Post-filter'
Configuration: CNVkit v0.9.7, post-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	2710 Count (exon level; reference CMA CNV exons in the evaluated set) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNVkit (post-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-post-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Reference Truth set', column 'CNVkit' / 'Post-filter'
Configuration: CNVkit v0.9.7, post-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.68 Recall (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNVkit (post-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-post-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Sensitivity', column 'CNVkit' / 'Post-filter'
Configuration: CNVkit v0.9.7, post-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	1840 True positives (exon level) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNVkit (post-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-post-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'TP', column 'CNVkit' / 'Post-filter'

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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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

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Technical metadata and extraction receipts

Stable ID: cnv-20261011-hwang2026-config-cnvkit-post-filter

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: CNVkit (post-filter)
foundation model eligible: false
version: v0.9.7
parameters: default parameters; CNV calls overlapping the tool's problematic regions removed (regions where the tool called CNVs in more than 10% of the 180-sample WES cohort; Methods 2.5)
access reuse: Open-source tool
source locator: Methods 2.3 and 2.5; Table 4 column header

Related records

configuration of: CNVkit
system: CNVkit (post-filter) on 39 clinical exomes against CMA truth

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