Protocol

Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4)

Area under the precision-recall curve for tumour-only calling: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs.

9 evaluations · 27 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

9 recorded evaluations, 27 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

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

All evaluations

9 evaluations · 27 results. Different protocols are not a single leaderboard.

Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) · Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x

Sorted by AUPRC (SNV only, tumour-only, AML sample) (higher 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	AUPRC (SNV only, tumour-only, AML sample)	AUPRC (SNV only, tumour-only, CLL sample)	AUPRC (SNV only, tumour-only, MBL sample)
VarNet-T, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.112 (best in column)	0.062 (best in column)	0.032 (best in column)
ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.04	0.031	0.012
DeepSom-LINC, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.033	0.024	0.021
DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.011	0.028	0.014
DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.01	0.029	0.014
DeepSom-LAML, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.006	0.007	0.006
Deepsomatic (tumor-only) v1.7.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.004	0.005	0.003
DeepSom-GACA, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.003	0.018	0.008
Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.002	0.002	0.002

All 27 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.04 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ClairS-TO on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'ClairS-TO', column 'AML'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.031 AUPRC (SNV only, tumour-only, CLL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ClairS-TO on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'ClairS-TO', column 'CLL'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.012 AUPRC (SNV only, tumour-only, MBL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ClairS-TO on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'ClairS-TO', column 'MBL'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.01 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-BLCA on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-BLCA', column 'AML'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.029 AUPRC (SNV only, tumour-only, CLL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-BLCA on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-BLCA', column 'CLL'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.014 AUPRC (SNV only, tumour-only, MBL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-BLCA on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-BLCA', column 'MBL'
Configuration: DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.011 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-ESAD on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-ESAD', column 'AML'
Configuration: DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.028 AUPRC (SNV only, tumour-only, CLL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-ESAD on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-ESAD', column 'CLL'
Configuration: DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.014 AUPRC (SNV only, tumour-only, MBL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-ESAD on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-ESAD', column 'MBL'
Configuration: DeepSom-GACA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.003 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-GACA on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-GACA', column 'AML'
Configuration: DeepSom-GACA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.018 AUPRC (SNV only, tumour-only, CLL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-GACA on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-GACA', column 'CLL'
Configuration: DeepSom-GACA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.008 AUPRC (SNV only, tumour-only, MBL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-GACA on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-GACA', column 'MBL'
Configuration: DeepSom-LAML, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.006 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-LAML on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-LAML', column 'AML'
Configuration: DeepSom-LAML, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.007 AUPRC (SNV only, tumour-only, CLL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-LAML on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-LAML', column 'CLL'
Configuration: DeepSom-LAML, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.006 AUPRC (SNV only, tumour-only, MBL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-LAML on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-LAML', column 'MBL'
Configuration: DeepSom-LINC, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.033 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-LINC on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-LINC', column 'AML'
Configuration: DeepSom-LINC, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.024 AUPRC (SNV only, tumour-only, CLL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-LINC on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-LINC', column 'CLL'
Configuration: DeepSom-LINC, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.021 AUPRC (SNV only, tumour-only, MBL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSom-LINC on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'DeepSom-LINC', column 'MBL'
Configuration: Deepsomatic (tumor-only) v1.7.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.004 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Deepsomatic (tumor-only) on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'Deepsomatic (tumor-only)', column 'AML'
Configuration: Deepsomatic (tumor-only) v1.7.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.005 AUPRC (SNV only, tumour-only, CLL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Deepsomatic (tumor-only) on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'Deepsomatic (tumor-only)', column 'CLL'
Configuration: Deepsomatic (tumor-only) v1.7.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.003 AUPRC (SNV only, tumour-only, MBL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Deepsomatic (tumor-only) on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'Deepsomatic (tumor-only)', column 'MBL'
Configuration: Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.002 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 (tumor-only) on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'Mutect2 (tumor-only)', column 'AML'
Configuration: Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.002 AUPRC (SNV only, tumour-only, CLL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 (tumor-only) on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'Mutect2 (tumor-only)', column 'CLL'
Configuration: Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.002 AUPRC (SNV only, tumour-only, MBL sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 (tumor-only) on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'Mutect2 (tumor-only)', column 'MBL'
Configuration: VarNet-T, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4) Dataset: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	0.112 AUPRC (SNV only, tumour-only, AML sample) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source VarNet-T on low-tmb-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-low-tmb-snv Aggregation: Not reported Improved tumor-only variant calling and mutation burden estimation with VarNet-T; VarNet-T Supplementary Information; VarNet-T Source Data workbook · Supplementary Table 4, row 'VarNet-T', column 'AML'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 1
External evaluations: 8

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

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.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

3 source records and release history

Improved tumor-only variant calling and mutation burden estimation with VarNet-T · Original source · Nature Communications, published 2026-04-09; PMC13243554 full-text XML
VarNet-T Supplementary Information · Original source · Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages
VarNet-T Source Data workbook · Original source · Source Data file (41467_2026_71705_MOESM6_ESM.xlsx)

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: somatic-varnet-t-20261011-protocol-low-tmb-snv

areas: dna-genomes
contexts: clinical_research
protocol: Tumour BAM only; each caller's score (VarNet-T score, Mutect2 TLOD, DeepSomatic QUAL, DeepSom cnn_score, ClairS-TO QUAL) is varied to trace a precision-recall curve against the truth set; AUPRC reported.
version: Supplementary Table 4
metric: auprc
limitations: Developer paper: the authors developed VarNet-T (and earlier VarNet); its rows are author_reported. Comparators were run by the authors.; Tumour-only calling: the matched normal was used only to build the truth sets, not by the callers.; Only AUPRC is extracted; the threshold-optimised best F1 values are shown in figures only.; No interval estimates.; About 1,200 truth SNVs per sample; the same CLL, MBL and AML samples underlie the Wang et al. 2020 tumour-normal protocols already linked, but here they are downsampled and called tumour-only.; DeepSom-LAML was trained on TCGA acute myeloid leukaemia data (Methods; Discussion); whether this AML sample is in its training data is not stated.
source locator: Supplementary Table 4; Methods 'Implementation of tumor-only variant callers' and 'Performance metrics'

Related records

uses data: ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x
assessment: ClairS-TO on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-BLCA on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-ESAD on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-GACA on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-LAML on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-LINC on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessment: Deepsomatic (tumor-only) on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessment: Mutect2 (tumor-only) on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessment: VarNet-T on low-tmb-snv tumour-only (Krishnamachari et al. 2026)
assessed by: Select a tumour DNA somatic variant-calling workflow

Suggest a correction