Protocol

PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2)

Area under the precision-recall curve for tumour-only calling: PCAWG ten primary tumours, tumour-only SNVs.

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, 90 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 · 90 results. Different protocols are not a single leaderboard.

Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) · Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training

Sorted by AUPRC (SNV only, tumour-only, PCAWG DO14566 (head and neck)) (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, PCAWG DO14566 (head and neck))	AUPRC (SNV only, tumour-only, PCAWG DO15046 (head and neck))	AUPRC (SNV only, tumour-only, PCAWG DO1663 (breast))	AUPRC (SNV only, tumour-only, PCAWG DO38423 (stomach))	AUPRC (SNV only, tumour-only, PCAWG DO38547 (stomach))	AUPRC (SNV only, tumour-only, PCAWG DO41056 (uterine))	AUPRC (SNV only, tumour-only, PCAWG DO41398 (uterine))	AUPRC (SNV only, tumour-only, PCAWG DO522 (bladder))	AUPRC (SNV only, tumour-only, PCAWG DO6144 (breast))	AUPRC (SNV only, tumour-only, PCAWG DO804 (bladder))
DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.756 (best in column)	0.423	0.734	0.143	0.621	0.294	0.493	0.706	0.718	0.715
VarNet-T, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.728	0.702 (best in column)	0.775 (best in column)	0.771 (best in column)	0.764 (best in column)	0.313	0.619 (best in column)	0.75 (best in column)	0.755 (best in column)	0.736 (best in column)
DeepSom-GACA, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.674	0.287	0.594	0.169	0.637	0.417 (best in column)	0.363	0.663	0.45	0.511
DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.645	0.452	0.704	0.277	0.674	0.273	0.543	0.603	0.643	0.561
DeepSom-LINC, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.619	0.425	0.612	0.269	0.6	0.315	0.398	0.612	0.626	0.586
ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.442	0.318	0.591	0.479	0.403	0.139	0.055	0.391	0.383	0.381
DeepSom-LAML, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.233	0.097	0.157	0.112	0.373	0.079	0.101	0.336	0.23	0.249
Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.202	0.049	0.154	0.07	0.173	0.097	0.099	0.126	0.148	0.172
Deepsomatic (tumor-only) v1.7.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	0.2	0.052	0.141	0.175	0.194	0.024	0.063	0.104	0.22	0.148

All 90 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: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.442 AUPRC (SNV only, tumour-only, PCAWG DO14566 (head and neck)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO14566'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.318 AUPRC (SNV only, tumour-only, PCAWG DO15046 (head and neck)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO15046'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.591 AUPRC (SNV only, tumour-only, PCAWG DO1663 (breast)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO1663'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.479 AUPRC (SNV only, tumour-only, PCAWG DO38423 (stomach)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO38423'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.403 AUPRC (SNV only, tumour-only, PCAWG DO38547 (stomach)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO38547'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.139 AUPRC (SNV only, tumour-only, PCAWG DO41056 (uterine)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO41056'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.055 AUPRC (SNV only, tumour-only, PCAWG DO41398 (uterine)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO41398'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.391 AUPRC (SNV only, tumour-only, PCAWG DO522 (bladder)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO522'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.383 AUPRC (SNV only, tumour-only, PCAWG DO6144 (breast)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO6144'
Configuration: ClairS-TO v0.4.0, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.381 AUPRC (SNV only, tumour-only, PCAWG DO804 (bladder)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'ClairS-TO (tumor-only)', column 'DO804'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.756 AUPRC (SNV only, tumour-only, PCAWG DO14566 (head and neck)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO14566'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.423 AUPRC (SNV only, tumour-only, PCAWG DO15046 (head and neck)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO15046'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.734 AUPRC (SNV only, tumour-only, PCAWG DO1663 (breast)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO1663'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.143 AUPRC (SNV only, tumour-only, PCAWG DO38423 (stomach)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO38423'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.621 AUPRC (SNV only, tumour-only, PCAWG DO38547 (stomach)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO38547'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.294 AUPRC (SNV only, tumour-only, PCAWG DO41056 (uterine)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO41056'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.493 AUPRC (SNV only, tumour-only, PCAWG DO41398 (uterine)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO41398'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.706 AUPRC (SNV only, tumour-only, PCAWG DO522 (bladder)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO522'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.718 AUPRC (SNV only, tumour-only, PCAWG DO6144 (breast)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO6144'
Configuration: DeepSom-BLCA, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.715 AUPRC (SNV only, tumour-only, PCAWG DO804 (bladder)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-BLCA', column 'DO804'
Configuration: DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.645 AUPRC (SNV only, tumour-only, PCAWG DO14566 (head and neck)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-ESAD', column 'DO14566'
Configuration: DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.452 AUPRC (SNV only, tumour-only, PCAWG DO15046 (head and neck)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-ESAD', column 'DO15046'
Configuration: DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.704 AUPRC (SNV only, tumour-only, PCAWG DO1663 (breast)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-ESAD', column 'DO1663'
Configuration: DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.277 AUPRC (SNV only, tumour-only, PCAWG DO38423 (stomach)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-ESAD', column 'DO38423'
Configuration: DeepSom-ESAD, tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2) Dataset: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	0.674 AUPRC (SNV only, tumour-only, PCAWG DO38547 (stomach)) 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 pcawg-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-pcawg-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 2, row 'DeepSom-ESAD', column 'DO38547'

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

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Author-reported evaluations: 1
External evaluations: 8

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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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)

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Technical metadata and extraction receipts

Stable ID: somatic-varnet-t-20261011-protocol-pcawg-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 2
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.; Truth is PCAWG consensus calls, themselves produced by tumour-normal callers.; Samples chosen with 10k to 100k SNVs; lower-burden tumours are covered only by the low-TMB protocol.; The source says the PCAWG cancer types were not used in training (Results; Methods 'PCAWG benchmark samples'), but its training cohort includes 38 gastric tumours (Methods 'Training data'); VarNet-T is not held out at cancer-type level for the two stomach samples DO38547 and DO38423.; DeepSom's BLCA-US and GACA-CN models were trained on ICGC projects of the same cancer types as the bladder (DO804, DO522) and stomach (DO38547, DO38423) test samples; the source does not say whether those donors were in DeepSom's training data.
source locator: Supplementary Table 2; Methods 'Implementation of tumor-only variant callers' and 'Performance metrics'

Related records

uses data: PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training
assessment: ClairS-TO on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-BLCA on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-ESAD on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-GACA on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-LAML on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessment: DeepSom-LINC on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessment: Deepsomatic (tumor-only) on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessment: Mutect2 (tumor-only) on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessment: VarNet-T on pcawg-snv tumour-only (Krishnamachari et al. 2026)
assessed by: Select a tumour DNA somatic variant-calling workflow

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