Published CNV caller comparison; transcribed, not reproduced.
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1 evaluation · 2 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Control-FREEC (Gabrielaite et al. WGS) | Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set | 0.267 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcecnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K175; sample GB-WGS-NA12878; tool ControlFREEC; column precision |
| Configuration: Control-FREEC (Gabrielaite et al. WGS) | Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set | 0.107 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcecnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L175; sample GB-WGS-NA12878; tool ControlFREEC; column recall |
Source checking is not independent reproduction. Release 2026-10-09-9307685239b3.
cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap
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36 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation Not reported Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) 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 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.adaptation Not reported Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
| attributes.comparison.aggregation Single sample Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation Single sample Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
| attributes.comparison.budget Not reported Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) 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 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.budget Not reported Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
| attributes.comparison.dataset_version Haraksingh et al. 2017 NA12878 CNV set Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.dataset_version Haraksingh et al. 2017 NA12878 CNV set Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
| attributes.comparison.inputs NA12878 WGS >=30x, BWA-MEM hg19 Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.inputs NA12878 WGS >=30x, BWA-MEM hg19 Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Table S2.xlsx, sheet Supplementary_table2, row 175 (sample GB-WGS-NA12878, tool ControlFREEC) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
Release 2026-10-09-9307685239b3 · Record review: source checked
Stable ID: cnv-20261009-eval-gabrielaite2021-control-freec-na12878-wgs