Protocol

DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1)

Per-caller recall, precision and F1 for somatic SNVs on one WGS tumour-normal pair.

Overview

Per-caller recall, precision and F1 for somatic SNVs on one WGS tumour-normal pair.

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

15 recorded evaluations, 60 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

15 evaluations · 60 results. Different protocols are not a single leaderboard.

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: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	6770 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LoFreq on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', D37; dataset 'DREAM Set3'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.913 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LoFreq on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', G37; dataset 'DREAM Set3'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.99 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LoFreq on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', F37; dataset 'DREAM Set3'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.847 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LoFreq on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', E37; dataset 'DREAM Set3'; caller 'LoFreq'; column 'Recall'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	7250 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuSE on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', D34; dataset 'DREAM Set3'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.918 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuSE on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', G34; dataset 'DREAM Set3'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.959 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuSE on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', F34; dataset 'DREAM Set3'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.88 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuSE on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', E34; dataset 'DREAM Set3'; caller 'MuSE'; column 'Recall'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	9980 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuTect on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', D41; dataset 'DREAM Set3'; caller 'MuTect'; column 'Count'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.823 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuTect on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', G41; dataset 'DREAM Set3'; caller 'MuTect'; column 'F1'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.738 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuTect on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', F41; dataset 'DREAM Set3'; caller 'MuTect'; column 'Precision'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.931 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuTect on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', E41; dataset 'DREAM Set3'; caller 'MuTect'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	8690 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MuTect2 on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', D42; dataset 'DREAM Set3'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.889 f1-score 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 on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', G42; dataset 'DREAM Set3'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.849 precision 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 on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', F42; dataset 'DREAM Set3'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.933 recall 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 on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', E42; dataset 'DREAM Set3'; caller 'MuTect2'; column 'Recall'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	12900 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NeuSomatic_Lowqual on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', D47; dataset 'DREAM Set3'; caller 'NeuSomatic_Lowqual'; column 'Count'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.735 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NeuSomatic_Lowqual on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', G47; dataset 'DREAM Set3'; caller 'NeuSomatic_Lowqual'; column 'F1'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.594 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NeuSomatic_Lowqual on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', F47; dataset 'DREAM Set3'; caller 'NeuSomatic_Lowqual'; column 'Precision'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.966 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NeuSomatic_Lowqual on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', E47; dataset 'DREAM Set3'; caller 'NeuSomatic_Lowqual'; column 'Recall'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	10000 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NeuSomatic_Pass on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', D48; dataset 'DREAM Set3'; caller 'NeuSomatic_Pass'; column 'Count'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.848 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NeuSomatic_Pass on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', G48; dataset 'DREAM Set3'; caller 'NeuSomatic_Pass'; column 'F1'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.758 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NeuSomatic_Pass on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', F48; dataset 'DREAM Set3'; caller 'NeuSomatic_Pass'; column 'Precision'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.962 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NeuSomatic_Pass on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', E48; dataset 'DREAM Set3'; caller 'NeuSomatic_Pass'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	12200 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-snv Aggregation: Not reported SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach; Wang et al. 2020, Supplementary Tables (somatic caller performance) · Supplementary Tables workbook sheet 'S1 WGS SNVs', D38; dataset 'DREAM Set3'; caller 'SomaticSniper'; column 'Count'

Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Explore all linked results

Baseline coverage

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

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

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

Author-reported evaluations: 4
External evaluations: 11

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

Null control

Proposed control: requires review

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

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

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

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

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

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

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

Coverage is derived from release 2026-10-09-8cc1db47c7f9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

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

Strengths, limitations and unresolved questions

Evidence

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

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

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

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-8cc1db47c7f9
Property and statement	Original source and location	Review and provenance

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

All evidence (JSONL) (gzip)How to read the evidence

Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

2 source records and release history

SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach · Original source · Scientific Reports 10:12898, published 2020-07-30; PMC7393490 full-text XML
Wang et al. 2020, Supplementary Tables (somatic caller performance) · Original source · 41598_2020_69772_MOESM3_ESM.xlsx (Supplementary Tables S1-S9) as served by the publisher

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: somatic-20261009-protocol-wang2020-dream-set3-snv

areas: dna-genomes
contexts: clinical_research
protocol: Callers run on the tumour-normal pair with default settings or author instructions; calls compared with the truth set by the DREAM challenge evaluator.py. Recall = detected true variants / true variants; precision = detected true variants / all calls.
version: Supplementary S1 WGS SNVs, dataset 'DREAM Set3'
metric implementation: evaluator.py from Sage-Bionetworks/ICGC-TCGA-DREAM-Mutation-Calling-challenge-tools (commit not stated)
denominator: 7903
limitations: Single tumour-normal pair; no replicate or interval estimates.; Synthetic tumour with mutations configured by a read simulator (Results 'Datasets for evaluation'); the authors contrast it with real datasets that 'reflect more complex variations and artifacts generated from real sequencing reads'.; 100% tumour cellularity with subclones (Methods 'Data collection').; No true variant below 10% VAF in DREAM sets 1 to 3 (Discussion paragraph 5), so low-VAF sensitivity is not tested.; NeuSomatic rows are excluded from this judgement: the model used was trained on DREAM set 3 (Results 'Evaluation of our consensus approach' paragraph 2).; Caller versions are those listed in Methods (for example MuTect2 from GATK v3.7-0, Strelka v2.7.1); later releases may behave differently.
source locator: Supplementary Tables workbook sheet 'S1 WGS SNVs', rows for dataset 'DREAM Set3'; Methods 'Variant calling comparisons'

Related records

uses data: ICGC-TCGA DREAM synthetic set 3 (WGS)
assessment: LoFreq on DREAM Set3 SNVs (Wang et al. 2020)
assessment: MuSE on DREAM Set3 SNVs (Wang et al. 2020)
assessment: MuTect on DREAM Set3 SNVs (Wang et al. 2020)
assessment: MuTect2 on DREAM Set3 SNVs (Wang et al. 2020)
assessment: NeuSomatic_Lowqual on DREAM Set3 SNVs (Wang et al. 2020)
assessment: NeuSomatic_Pass on DREAM Set3 SNVs (Wang et al. 2020)
assessment: SomaticSniper on DREAM Set3 SNVs (Wang et al. 2020)
assessment: Strelka on DREAM Set3 SNVs (Wang et al. 2020)
assessment: VarDict (bcbio) on DREAM Set3 SNVs (Wang et al. 2020)
assessment: VarDict (standalone) on DREAM Set3 SNVs (Wang et al. 2020)
assessment: VarScan on DREAM Set3 SNVs (Wang et al. 2020)
assessment: 4callers(voting>=2) on DREAM Set3 SNVs (Wang et al. 2020)
assessment: 4callers(voting>=3) on DREAM Set3 SNVs (Wang et al. 2020)
assessment: 7callers(voting>=3) on DREAM Set3 SNVs (Wang et al. 2020)
assessment: 7callers(voting>=4) on DREAM Set3 SNVs (Wang et al. 2020)
assessed by: Select a tumour DNA somatic variant-calling workflow

Suggest a correction