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DeepSom-GACA, tumour-only Illumina WGS (Krishnamachari et al. 2026)

DeepSom-GACA, tumour-only Illumina WGS: Pre-trained DeepSom model GACA-CN (gastric) on Mutect2 tumour-only candidates, with gnomAD and panel of normals; scored by cnn_score.

6 evaluations · 17 results

Overview

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

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))
DeepSom-GACA, 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	0.257 (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
DeepSom-GACA, 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)	0.016	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
DeepSom-GACA, 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	0.07	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
DeepSom-GACA, 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	0.003	0.018	0.008	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
DeepSom-GACA, 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	0.674	0.287	0.594	0.169	0.637	0.417	0.363	0.663	0.45	0.511
DeepSom-GACA, 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	0.246 (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: DeepSom-GACA, 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)	0.016 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 DeepSom-GACA 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 'DeepSom-GACA', column 'COLO829 INDEL'
Configuration: DeepSom-GACA, 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)	0.07 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 DeepSom-GACA 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 'DeepSom-GACA', column 'COLO829 SNV'
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-GACA, 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 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-GACA 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-GACA', column 'DO14566'
Configuration: DeepSom-GACA, 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	0.287 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-GACA 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-GACA', column 'DO15046'
Configuration: DeepSom-GACA, 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	0.594 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-GACA 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-GACA', column 'DO1663'
Configuration: DeepSom-GACA, 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	0.169 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-GACA 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-GACA', column 'DO38423'
Configuration: DeepSom-GACA, 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	0.637 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-GACA 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-GACA', column 'DO38547'
Configuration: DeepSom-GACA, 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	0.417 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-GACA 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-GACA', column 'DO41056'
Configuration: DeepSom-GACA, 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	0.363 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-GACA 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-GACA', column 'DO41398'
Configuration: DeepSom-GACA, 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	0.663 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-GACA 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-GACA', column 'DO522'
Configuration: DeepSom-GACA, 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	0.45 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-GACA 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-GACA', column 'DO6144'
Configuration: DeepSom-GACA, 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	0.511 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-GACA 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-GACA', column 'DO804'
Configuration: DeepSom-GACA, 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	0.257 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 DeepSom-GACA 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 'DeepSom-GACA', column 'SEQC2 INDEL'
Configuration: DeepSom-GACA, 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	0.246 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 DeepSom-GACA 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 'DeepSom-GACA', column 'SEQC2 SNV'

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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-deepsom-gaca

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: DeepSom-GACA
foundation model eligible: false
parameters: Pre-trained DeepSom model GACA-CN (gastric) on Mutect2 tumour-only candidates, with gnomAD and panel of normals; scored by cnn_score
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: DeepSom-GACA as run in the cited tumour-only comparison.

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