Method

CNVnator

Evidence concern: excluded from comparisons

Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13

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

Read-depth CNV caller.

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Overview

Read-depth CNV caller.

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Evidence

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Evidence table

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Sources and history

Release 2026-10-09-8eac2440869c · Record review: source checked

8 source records and release history

Comprehensive genome analysis and variant detection at scale using DRAGEN · Original source · 2024-10-25 version of record; code-availability correction 2024-12-02; July 2025 issue
DRAGEN supplementary tables 1–17 · Original source · MOESM3 XLSX retrieved 2026-10-07
Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Original source · Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML
De La Vega et al. 2025, Supplemental Table 3 · Original source · Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip
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
Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Original source · Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip
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-method-cnvnator

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: CNVnator
entity level: method
source locator: Tool lists and table row labels of the cited sources
missing metadata: version: reason: unreported; note: Family record; versions are on configurations

Related records

configuration of: CNVnator comparator (Behera et al. Table S4)
configuration of: CNVnator v0.4.1 (De La Vega et al.)
configuration of: CNVnator (Gabrielaite et al. WGS)
configuration of: CNVnator v0.4.1 (Nardone et al.)

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