Protocol

DREAM synthetic set 4 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.

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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.

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Results

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All evaluations

15 evaluations · 60 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: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	7540 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D52; dataset 'DREAM Set4'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.623 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G52; dataset 'DREAM Set4'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.983 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F52; dataset 'DREAM Set4'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.456 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E52; dataset 'DREAM Set4'; caller 'LoFreq'; column 'Recall'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	10300 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D49; dataset 'DREAM Set4'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.673 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G49; dataset 'DREAM Set4'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.869 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F49; dataset 'DREAM Set4'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.55 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E49; dataset 'DREAM Set4'; caller 'MuSE'; column 'Recall'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	14800 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D56; dataset 'DREAM Set4'; caller 'MuTect'; column 'Count'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.782 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G56; dataset 'DREAM Set4'; caller 'MuTect'; column 'F1'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.82 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F56; dataset 'DREAM Set4'; caller 'MuTect'; column 'Precision'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.747 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E56; dataset 'DREAM Set4'; caller 'MuTect'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	13500 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D57; dataset 'DREAM Set4'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.825 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G57; dataset 'DREAM Set4'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.911 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F57; dataset 'DREAM Set4'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.755 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E57; dataset 'DREAM Set4'; caller 'MuTect2'; column 'Recall'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	20400 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D62; dataset 'DREAM Set4'; caller 'NeuSomatic_Lowqual'; column 'Count'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.783 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G62; dataset 'DREAM Set4'; caller 'NeuSomatic_Lowqual'; column 'F1'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.704 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F62; dataset 'DREAM Set4'; caller 'NeuSomatic_Lowqual'; column 'Precision'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.881 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E62; dataset 'DREAM Set4'; caller 'NeuSomatic_Lowqual'; column 'Recall'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	16600 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D63; dataset 'DREAM Set4'; caller 'NeuSomatic_Pass'; column 'Count'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.859 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G63; dataset 'DREAM Set4'; caller 'NeuSomatic_Pass'; column 'F1'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (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 NeuSomatic_Pass on DREAM Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F63; dataset 'DREAM Set4'; caller 'NeuSomatic_Pass'; column 'Precision'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.868 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E63; dataset 'DREAM Set4'; caller 'NeuSomatic_Pass'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	16500 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 Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D53; dataset 'DREAM Set4'; caller 'SomaticSniper'; column 'Count'

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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

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Technical metadata and extraction receipts

Stable ID: somatic-20261009-protocol-wang2020-dream-set4-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 Set4'
metric implementation: evaluator.py from Sage-Bionetworks/ICGC-TCGA-DREAM-Mutation-Calling-challenge-tools (commit not stated)
denominator: 16315
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'.; 80% tumour cellularity with subclones; only DREAM set with a few true variants below 10% VAF (Methods 'Data collection'; Discussion paragraph 5).; The NeuSomatic model was trained on DREAM set 3, made by the same simulator; the authors attribute NeuSomatic's high set 4 F1 to this (Results 'Evaluation of our consensus approach' paragraph 2; Supplementary Fig. S13 PCA).; 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 Set4'; Methods 'Variant calling comparisons'

Related records

uses data: ICGC-TCGA DREAM synthetic set 4 (WGS)
assessment: LoFreq on DREAM Set4 SNVs (Wang et al. 2020)
assessment: MuSE on DREAM Set4 SNVs (Wang et al. 2020)
assessment: MuTect on DREAM Set4 SNVs (Wang et al. 2020)
assessment: MuTect2 on DREAM Set4 SNVs (Wang et al. 2020)
assessment: NeuSomatic_Lowqual on DREAM Set4 SNVs (Wang et al. 2020)
assessment: NeuSomatic_Pass on DREAM Set4 SNVs (Wang et al. 2020)
assessment: SomaticSniper on DREAM Set4 SNVs (Wang et al. 2020)
assessment: Strelka on DREAM Set4 SNVs (Wang et al. 2020)
assessment: VarDict (bcbio) on DREAM Set4 SNVs (Wang et al. 2020)
assessment: VarDict (standalone) on DREAM Set4 SNVs (Wang et al. 2020)
assessment: VarScan on DREAM Set4 SNVs (Wang et al. 2020)
assessment: 4callers(voting>=2) on DREAM Set4 SNVs (Wang et al. 2020)
assessment: 4callers(voting>=3) on DREAM Set4 SNVs (Wang et al. 2020)
assessment: 7callers(voting>=3) on DREAM Set4 SNVs (Wang et al. 2020)
assessment: 7callers(voting>=4) on DREAM Set4 SNVs (Wang et al. 2020)
assessed by: Select a tumour DNA somatic variant-calling workflow

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