Protocol

DREAM synthetic set 2 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 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	4190 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', D22; dataset 'DREAM Set2'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.96 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', G22; dataset 'DREAM Set2'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.974 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', F22; dataset 'DREAM Set2'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.945 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', E22; dataset 'DREAM Set2'; caller 'LoFreq'; column 'Recall'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	4630 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', D19; dataset 'DREAM Set2'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.938 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', G19; dataset 'DREAM Set2'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.907 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', F19; dataset 'DREAM Set2'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.971 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', E19; dataset 'DREAM Set2'; caller 'MuSE'; column 'Recall'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	7370 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', D26; dataset 'DREAM Set2'; caller 'MuTect'; column 'Count'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.722 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', G26; dataset 'DREAM Set2'; caller 'MuTect'; column 'F1'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.573 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', F26; dataset 'DREAM Set2'; caller 'MuTect'; column 'Precision'
Configuration: MuTect v1.1.7 (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.977 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', E26; dataset 'DREAM Set2'; caller 'MuTect'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	6080 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', D27; dataset 'DREAM Set2'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.813 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', G27; dataset 'DREAM Set2'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.695 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', F27; dataset 'DREAM Set2'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.978 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', E27; dataset 'DREAM Set2'; caller 'MuTect2'; column 'Recall'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	11200 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', D32; dataset 'DREAM Set2'; caller 'NeuSomatic_Lowqual'; column 'Count'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.551 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', G32; dataset 'DREAM Set2'; caller 'NeuSomatic_Lowqual'; column 'F1'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.382 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', F32; dataset 'DREAM Set2'; caller 'NeuSomatic_Lowqual'; column 'Precision'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, all calls (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.991 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', E32; dataset 'DREAM Set2'; caller 'NeuSomatic_Lowqual'; column 'Recall'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	7810 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', D33; dataset 'DREAM Set2'; caller 'NeuSomatic_Pass'; column 'Count'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.705 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', G33; dataset 'DREAM Set2'; caller 'NeuSomatic_Pass'; column 'F1'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.548 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', F33; dataset 'DREAM Set2'; caller 'NeuSomatic_Pass'; column 'Precision'
Configuration: NeuSomatic v0.2.1 ensemble mode, DREAM3 model, PASS calls (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	0.99 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', E33; dataset 'DREAM Set2'; caller 'NeuSomatic_Pass'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	10200 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-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', D23; dataset 'DREAM Set2'; 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-set2-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 Set2'
metric implementation: evaluator.py from Sage-Bionetworks/ICGC-TCGA-DREAM-Mutation-Calling-challenge-tools (commit not stated)
denominator: 4332
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, no 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.; 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 Set2'; Methods 'Variant calling comparisons'

Related records

uses data: ICGC-TCGA DREAM synthetic set 2 (WGS)
assessment: LoFreq on DREAM Set2 SNVs (Wang et al. 2020)
assessment: MuSE on DREAM Set2 SNVs (Wang et al. 2020)
assessment: MuTect on DREAM Set2 SNVs (Wang et al. 2020)
assessment: MuTect2 on DREAM Set2 SNVs (Wang et al. 2020)
assessment: NeuSomatic_Lowqual on DREAM Set2 SNVs (Wang et al. 2020)
assessment: NeuSomatic_Pass on DREAM Set2 SNVs (Wang et al. 2020)
assessment: SomaticSniper on DREAM Set2 SNVs (Wang et al. 2020)
assessment: Strelka on DREAM Set2 SNVs (Wang et al. 2020)
assessment: VarDict (bcbio) on DREAM Set2 SNVs (Wang et al. 2020)
assessment: VarDict (standalone) on DREAM Set2 SNVs (Wang et al. 2020)
assessment: VarScan on DREAM Set2 SNVs (Wang et al. 2020)
assessment: 4callers(voting>=2) on DREAM Set2 SNVs (Wang et al. 2020)
assessment: 4callers(voting>=3) on DREAM Set2 SNVs (Wang et al. 2020)
assessment: 7callers(voting>=3) on DREAM Set2 SNVs (Wang et al. 2020)
assessment: 7callers(voting>=4) on DREAM Set2 SNVs (Wang et al. 2020)
assessed by: Select a tumour DNA somatic variant-calling workflow

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