Configuration

Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)

Mutect2 (tumor-only), tumour-only Illumina WGS: Tumour-only mode with gnomAD v4.1 germline resource and the GATK 1000g hg38 panel of normals; scored by TLOD.

6 evaluations · 17 results

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Evaluations and results

6 evaluations · 17 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (indel only, tumour-only) (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	Protocol and dataset	AUPRC (indel only, tumour-only)	AUPRC (SNV only, tumour-only)	AUPRC (SNV only, tumour-only, AML sample)	AUPRC (SNV only, tumour-only, CLL sample)	AUPRC (SNV only, tumour-only, MBL sample)	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))
Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	SEQC2 HCC1395 tumour-only, indels, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1), SEQC2 HCC1395 tumour Illumina HiSeq WGS (WGS_IL_T_1), high-confidence regions	0.003 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	COLO829 tumour-only, indels, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1), COLO829 tumour Illumina WGS (TGen reference set)	0.002	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	COLO829 tumour-only, SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1), COLO829 tumour Illumina WGS (TGen reference set)	Not reported	0.072	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	Low-mutation-burden tumours (AML, MBL, CLL), tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 4), ICGC CLL and medulloblastoma and an AML tumour WGS, downsampled to about 100x	Not reported	Not reported	0.002	0.002	0.002	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	PCAWG ten primary tumours, tumour-only SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 2), PCAWG primary tumour WGS, ten samples from five cancer types not used in VarNet-T training	Not reported	Not reported	Not reported	Not reported	Not reported	0.202	0.049	0.154	0.07	0.173	0.097	0.099	0.126	0.148	0.172
Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)Evaluation	SEQC2 HCC1395 tumour-only, SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1), SEQC2 HCC1395 tumour Illumina HiSeq WGS (WGS_IL_T_1), high-confidence regions	Not reported	0.078 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 17 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: COLO829 tumour-only, indels, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1) Dataset: COLO829 tumour Illumina WGS (TGen reference set)	0.002 AUPRC (indel only, tumour-only) 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 colo829-indel tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-colo829-indel 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 1, row 'Mutect2 (tumor-only)', column 'COLO829 INDEL'
Configuration: Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: COLO829 tumour-only, SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1) Dataset: COLO829 tumour Illumina WGS (TGen reference set)	0.072 AUPRC (SNV only, tumour-only) 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 colo829-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-colo829-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 1, row 'Mutect2 (tumor-only)', column 'COLO829 SNV'
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: Mutect2 (tumor-only), 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	0.202 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO14566'
Configuration: Mutect2 (tumor-only), 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	0.049 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO15046'
Configuration: Mutect2 (tumor-only), 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	0.154 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO1663'
Configuration: Mutect2 (tumor-only), 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	0.07 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO38423'
Configuration: Mutect2 (tumor-only), 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	0.173 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO38547'
Configuration: Mutect2 (tumor-only), 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	0.097 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO41056'
Configuration: Mutect2 (tumor-only), 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	0.099 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO41398'
Configuration: Mutect2 (tumor-only), 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	0.126 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO522'
Configuration: Mutect2 (tumor-only), 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	0.148 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO6144'
Configuration: Mutect2 (tumor-only), 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	0.172 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 Mutect2 (tumor-only) 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 'Mutect2 (tumor-only)', column 'DO804'
Configuration: Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: SEQC2 HCC1395 tumour-only, indels, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1) Dataset: SEQC2 HCC1395 tumour Illumina HiSeq WGS (WGS_IL_T_1), high-confidence regions	0.003 AUPRC (indel only, tumour-only) 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 seqc2-indel tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-seqc2-indel 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 1, row 'Mutect2 (tumor-only)', column 'SEQC2 INDEL'
Configuration: Mutect2 (tumor-only), tumour-only Illumina WGS (Krishnamachari et al. 2026)	Protocol: SEQC2 HCC1395 tumour-only, SNVs, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1) Dataset: SEQC2 HCC1395 tumour Illumina HiSeq WGS (WGS_IL_T_1), high-confidence regions	0.078 AUPRC (SNV only, tumour-only) 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 seqc2-snv tumour-only (Krishnamachari et al. 2026) somatic-varnet-t-20261011-protocol-seqc2-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 1, row 'Mutect2 (tumor-only)', column 'SEQC2 SNV'

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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-config-mutect2-tumor-only

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Mutect2 (tumor-only)
foundation model eligible: false
parameters: Tumour-only mode with gnomAD v4.1 germline resource and the GATK 1000g hg38 panel of normals; scored by TLOD
access reuse: Public software and models
source locator: Methods 'Implementation of tumor-only variant callers'; Supplementary Tables 1, 2 and 4 row labels
missing metadata: version: reason: unreported
provenance note: Mutect2 (tumor-only) as run in the cited tumour-only comparison.

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