Dataset

PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training

Ten PCAWG primary tumours (breast, bladder, stomach, head and neck, uterine; 10k to 100k SNVs; at most 100x) used tumour-only; truth is the PCAWG expert-reviewed consensus calls.

Evaluation results

9 evaluations · 90 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: 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'

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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21 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
Accession PCAWG donors DO6144, DO1663, DO522, DO804, DO38547, DO38423, DO14566, DO15046, DO41398, DO41056 Context-only references	Improved tumor-only variant calling and mutation burden estimation with VarNet-T Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.accession` Source artifact SHA-256: `b42db521781cd548b5ce0cf99233f8e790781fb5e8953fe733202009dd8367bb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Accession PCAWG donors DO6144, DO1663, DO522, DO804, DO38547, DO38423, DO14566, DO15046, DO41398, DO41056 Context-only references	VarNet-T Source Data workbook Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2026_71705_MOESM6_ESM.xlsx) Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.accession` Source artifact SHA-256: `4a2deae733ff93a9ae0001053816d82fb60787b01646183c8d37fbc5a764cd17` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Accession PCAWG donors DO6144, DO1663, DO522, DO804, DO38547, DO38423, DO14566, DO15046, DO41398, DO41056 Context-only references	VarNet-T Supplementary Information Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.accession` Source artifact SHA-256: `c808b4361e17a64911a59ded81d9db04c7a3dd5ba95fb3e1e060a293182f2842` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay Illumina WGS aligned with BWA-MEM (bcbio-nextgen) to GRCh38 Context-only references	Improved tumor-only variant calling and mutation burden estimation with VarNet-T Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `b42db521781cd548b5ce0cf99233f8e790781fb5e8953fe733202009dd8367bb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay Illumina WGS aligned with BWA-MEM (bcbio-nextgen) to GRCh38 Context-only references	VarNet-T Source Data workbook Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2026_71705_MOESM6_ESM.xlsx) Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `4a2deae733ff93a9ae0001053816d82fb60787b01646183c8d37fbc5a764cd17` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay Illumina WGS aligned with BWA-MEM (bcbio-nextgen) to GRCh38 Context-only references	VarNet-T Supplementary Information Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `c808b4361e17a64911a59ded81d9db04c7a3dd5ba95fb3e1e060a293182f2842` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population Ten PCAWG primary tumours (breast, bladder, stomach, head and neck, uterine; 10k to 100k SNVs; at most 100x) Context-only references	Improved tumor-only variant calling and mutation burden estimation with VarNet-T Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `b42db521781cd548b5ce0cf99233f8e790781fb5e8953fe733202009dd8367bb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population Ten PCAWG primary tumours (breast, bladder, stomach, head and neck, uterine; 10k to 100k SNVs; at most 100x) Context-only references	VarNet-T Source Data workbook Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data file (41467_2026_71705_MOESM6_ESM.xlsx) Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `4a2deae733ff93a9ae0001053816d82fb60787b01646183c8d37fbc5a764cd17` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population Ten PCAWG primary tumours (breast, bladder, stomach, head and neck, uterine; 10k to 100k SNVs; at most 100x) Context-only references	VarNet-T Supplementary Information Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages Retrieved: 2026-10-11T21:51:40Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `c808b4361e17a64911a59ded81d9db04c7a3dd5ba95fb3e1e060a293182f2842` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Context-only references	Improved tumor-only variant calling and mutation burden estimation with VarNet-T Original source ↗ Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications, published 2026-04-09; PMC13243554 full-text XML Retrieved: 2026-10-11T21:37:39Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `b42db521781cd548b5ce0cf99233f8e790781fb5e8953fe733202009dd8367bb` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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)

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Technical metadata and extraction receipts

Stable ID: somatic-varnet-t-20261011-data-pcawg

areas: dna-genomes
contexts: clinical_research
population: Ten PCAWG primary tumours (breast, bladder, stomach, head and neck, uterine; 10k to 100k SNVs; at most 100x)
assay: Illumina WGS aligned with BWA-MEM (bcbio-nextgen) to GRCh38
accession: PCAWG donors DO6144, DO1663, DO522, DO804, DO38547, DO38423, DO14566, DO15046, DO41398, DO41056
split: Samples not used in VarNet-T training. The source says the five cancer types were not in the training cohorts, but the training cohort includes 38 gastric tumours and two test samples (DO38547, DO38423) are stomach adenocarcinomas.
source locator: Results 'Benchmarking on somatic reference datasets', 'Benchmarking using whole cancer genomes from PCAWG', 'Challenges in tumor samples with low somatic mutation burden'; Methods 'Sample processing and in silico dilutions', 'PCAWG benchmark samples'; Data availability
missing metadata: version: reason: unreported

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