Protocol

Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-filter)

As pre-filter, after removing calls in each tool's problematic regions; reference exons in those regions are also removed, so the reference count differs by tool (2,124 to 2,723 of 2,788).

4 evaluations · 24 results

Overview

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4 recorded evaluations, 24 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

4 evaluations · 24 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)
ExomeDepth v1.1.15, post-filter (Hwang et al. 2026)Evaluation	207 (best in column)	16,797	0.102	0.903 (best in column)	1917	2124
CoNIFER v0.2.2, post-filter (Hwang et al. 2026)Evaluation	620	6288	0.25 (best in column)	0.771	2093 (best in column)	2713
CNVkit v0.9.7, post-filter (Hwang et al. 2026)Evaluation	866	6578	0.219	0.68	1844	2710
cn.MOPS v1.14.1, post-filter (Hwang et al. 2026)Evaluation	2282	2628 (best in column)	0.144	0.162	441	2723

All 24 result rows with coverage, uncertainty and sources

Filter evaluations

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: cn.MOPS v1.14.1, 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)	2280 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 cn.MOPS (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 'cn.MOPS' / 'Post-filter'
Configuration: cn.MOPS v1.14.1, 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)	2630 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 cn.MOPS (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 'cn.MOPS' / 'Post-filter'
Configuration: cn.MOPS v1.14.1, 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)	0.144 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 cn.MOPS (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 'cn.MOPS' / 'Post-filter'
Configuration: cn.MOPS v1.14.1, 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)	2720 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 cn.MOPS (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 'cn.MOPS' / 'Post-filter'
Configuration: cn.MOPS v1.14.1, 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)	0.162 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 cn.MOPS (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 'cn.MOPS' / 'Post-filter'
Configuration: cn.MOPS v1.14.1, 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)	441 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 cn.MOPS (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 'cn.MOPS' / '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)	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'
Configuration: CoNIFER v0.2.2, 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)	620 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 CoNIFER (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 'CoNIFER' / 'Post-filter'
Configuration: CoNIFER v0.2.2, 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)	6290 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 CoNIFER (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 'CoNIFER' / 'Post-filter'
Configuration: CoNIFER v0.2.2, 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)	0.25 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 CoNIFER (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 'CoNIFER' / 'Post-filter'
Configuration: CoNIFER v0.2.2, 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 CoNIFER (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 'CoNIFER' / 'Post-filter'
Configuration: CoNIFER v0.2.2, 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)	0.771 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 CoNIFER (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 'CoNIFER' / 'Post-filter'
Configuration: CoNIFER v0.2.2, 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)	2090 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 CoNIFER (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 'CoNIFER' / 'Post-filter'
Configuration: ExomeDepth v1.1.15, 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)	207 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 ExomeDepth (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 'ExomeDepth' / 'Post-filter'
Configuration: ExomeDepth v1.1.15, 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)	16,797 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 ExomeDepth (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 'ExomeDepth' / 'Post-filter'
Configuration: ExomeDepth v1.1.15, 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)	0.102 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 ExomeDepth (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 'ExomeDepth' / 'Post-filter'
Configuration: ExomeDepth v1.1.15, 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)	2120 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 ExomeDepth (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 'ExomeDepth' / 'Post-filter'
Configuration: ExomeDepth v1.1.15, 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)	0.903 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 ExomeDepth (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 'ExomeDepth' / 'Post-filter'
Configuration: ExomeDepth v1.1.15, 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)	1920 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 ExomeDepth (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 'ExomeDepth' / 'Post-filter'

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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-protocol-post-filter

areas: dna-genomes
contexts: clinical_research
protocol: As pre-filter, after removing calls in each tool's problematic regions; reference exons in those regions are also removed, so the reference count differs by tool (2,124 to 2,723 of 2,788).
version: Table 4
source locator: Table 4; Methods 2.2, 2.4 and 2.5; Results 3.3
limitations: The filter is the authors' method and is defined on the same 180-sample cohort, including the 39 evaluated exomes.; The reference truth set shrinks after filtering (Table 4 row 'Reference Truth set'), so post-filter sensitivity is on fewer exons.; Exome input, not the whole-genome input this use case names.; Exon-level scoring against CMA-derived truth: CMA misses small CNVs and only CNVs overlapping exome baits were kept, so precision counts any exon call outside that truth as false.; 39 individuals from one centre; no uncertainty intervals are printed.

Related records

uses data: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)
assessment: cn.MOPS (post-filter) on 39 clinical exomes against CMA truth
assessment: CNVkit (post-filter) on 39 clinical exomes against CMA truth
assessment: CoNIFER (post-filter) on 39 clinical exomes against CMA truth
assessment: ExomeDepth (post-filter) on 39 clinical exomes against CMA truth
assessed by: Select a copy-number variant detection and characterisation workflow

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