Protocol

Lancet paper virtual-tumor SNV/indel benchmark

Lancet paper virtual-tumor SNV/indel benchmark; bounded primary-source AMP candidate.

Overview

Lancet paper virtual-tumor SNV/indel benchmark; bounded primary-source AMP candidate.

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2 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

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All evaluations

2 evaluations · 24 results. Different protocols are not a single leaderboard.

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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: 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Lancet evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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 checked Methods, coverage and source Strelka2 evaluation Separate 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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Author-reported evaluations: 1
External evaluations: 1

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Genome-wide somatic variant calling using localized colored de Bruijn graphs · Original source · Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00

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Technical metadata and extraction receipts

Stable ID: amp-oncology-rna-20261007-protocol-lancet-virtual-tumor

areas: dna-genomes
method types: conventional_pipeline
missing metadata: None recorded
scope note: Author-developed-caller evaluation, not independent reproduction. Virtual tumor endpoint does not establish sensitivity in clinical tumors, FFPE samples, panels, ctDNA, copy-number or structural variation. SNV printed counts agree with 31,592 truth variants. Do not repair MuTect table #calls=50,228 versus TP+FP=26,505; its row is not proposed for numerical ingestion. Indel Lancet and Strelka2 counts agree with 4,945 truth variants. Preserve Table 1 rounding and do not recompute percentages. Individual-condition confidence intervals unreported in Tables 1–2.
task: Separate 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.
version: 2018 primary article Tables 1–2

Related records

protocol: Lancet evaluation
protocol: Strelka2 evaluation

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