NA12892/NA12891 virtual tumor and matched normal; bounded primary-source AMP candidate.
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Release 2026-10-07-1448159e6a81 · Evidence verified: Not verified
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2 evaluations · 24 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.81 indel F1-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 1360 indel false negatives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 305 indel false positives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.92 indel precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.72 indel recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 3590 indel true positives variants · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.85 SNV F1-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 7740 SNV false negatives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 565 SNV false positives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.98 SNV precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.75 SNV recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 23,848 SNV true positives variants · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.77 indel F1-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Strelka2 row (JATS Tab1) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 1300 indel false negatives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Strelka2 row (JATS Tab1) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 867 indel false positives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Strelka2 row (JATS Tab1) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.81 indel precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Strelka2 row (JATS Tab1) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.73 indel recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Strelka2 row (JATS Tab1) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 3650 indel true positives variants · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Strelka2 row (JATS Tab1) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.85 SNV F1-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Strelka2 row (JATS Tab2) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 7460 SNV false negatives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Strelka2 row (JATS Tab2) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 1120 SNV false positives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Strelka2 row (JATS Tab2) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.96 SNV precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Strelka2 row (JATS Tab2) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.76 SNV recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Strelka2 row (JATS Tab2) |
| Configuration: Strelka2 | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 24,132 SNV true positives variants · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Strelka2 row (JATS Tab2) |
Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.
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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.
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7 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.accession Not reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | missing or unspecified No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.assay Illumina HiSeq X PCR-free WGS, 80× virtual tumor and 40× normal Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.population 31,592 spiked SNVs; 4,945 spiked indels; NA12892 and NA12891 HapMap samples Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.split constructed evaluation; no training/test split extracted Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.version Not reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | missing or unspecified No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| description NA12892/NA12891 virtual tumor and matched normal; bounded primary-source AMP candidate. Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| name NA12892/NA12891 virtual tumor and matched normal Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-10-07-1448159e6a81 · Record review: source checked
Stable ID: amp-oncology-rna-20261007-dataset-lancet-virtual-tumor