Protocol

DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2)

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

Overview

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

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12 recorded evaluations, 48 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

12 evaluations · 48 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 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	4760 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', D6; dataset 'DREAM Set3'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.704 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', G6; dataset 'DREAM Set3'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.944 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', F6; dataset 'DREAM Set3'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.562 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', E6; dataset 'DREAM Set3'; caller 'LoFreq'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	6070 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', D9; dataset 'DREAM Set3'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.812 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', G9; dataset 'DREAM Set3'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.94 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', F9; dataset 'DREAM Set3'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.714 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', E9; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	7800 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', D15; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.706 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', G15; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.715 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', F15; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.697 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', E15; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	6450 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', D14; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.732 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', G14; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (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 NeuSomatic_Pass on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', F14; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.661 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', E14; dataset 'DREAM Set3'; caller 'NeuSomatic_Pass'; column 'Recall'
Configuration: Strelka v2.7.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	5470 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 Strelka on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', D7; dataset 'DREAM Set3'; caller 'Strelka'; column 'Count'
Configuration: Strelka v2.7.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.761 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 Strelka on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', G7; dataset 'DREAM Set3'; caller 'Strelka'; column 'F1'
Configuration: Strelka v2.7.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.936 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 Strelka on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', F7; dataset 'DREAM Set3'; caller 'Strelka'; column 'Precision'
Configuration: Strelka v2.7.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.641 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 Strelka on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', E7; dataset 'DREAM Set3'; caller 'Strelka'; column 'Recall'
Configuration: VarDict through bcbio-nextgen v1.1.5 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	10400 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 VarDict (bcbio) on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', D4; dataset 'DREAM Set3'; caller 'VarDict (bcbio)'; column 'Count'
Configuration: VarDict through bcbio-nextgen v1.1.5 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.618 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 VarDict (bcbio) on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', G4; dataset 'DREAM Set3'; caller 'VarDict (bcbio)'; column 'F1'
Configuration: VarDict through bcbio-nextgen v1.1.5 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.545 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 VarDict (bcbio) on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', F4; dataset 'DREAM Set3'; caller 'VarDict (bcbio)'; column 'Precision'
Configuration: VarDict through bcbio-nextgen v1.1.5 (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.713 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 VarDict (bcbio) on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', E4; dataset 'DREAM Set3'; caller 'VarDict (bcbio)'; column 'Recall'
Configuration: VarDict v1.6.0 standalone (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	68700 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 VarDict (standalone) on DREAM Set3 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-indel 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 'S2 WGS INDELs', D5; dataset 'DREAM Set3'; caller 'VarDict (standalone)'; 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-set3-indel

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 S2 WGS INDELs, dataset 'DREAM Set3'
metric implementation: evaluator.py from Sage-Bionetworks/ICGC-TCGA-DREAM-Mutation-Calling-challenge-tools (commit not stated)
denominator: 7991
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 'S2 WGS INDELs', 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 indels (Wang et al. 2020)
assessment: MuTect2 on DREAM Set3 indels (Wang et al. 2020)
assessment: NeuSomatic_Lowqual on DREAM Set3 indels (Wang et al. 2020)
assessment: NeuSomatic_Pass on DREAM Set3 indels (Wang et al. 2020)
assessment: Strelka on DREAM Set3 indels (Wang et al. 2020)
assessment: VarDict (bcbio) on DREAM Set3 indels (Wang et al. 2020)
assessment: VarDict (standalone) on DREAM Set3 indels (Wang et al. 2020)
assessment: VarScan on DREAM Set3 indels (Wang et al. 2020)
assessment: 3callers (>=1) on DREAM Set3 indels (Wang et al. 2020)
assessment: 3callers (>=2) on DREAM Set3 indels (Wang et al. 2020)
assessment: 5callers (>=2) on DREAM Set3 indels (Wang et al. 2020)
assessment: 5callers (>=3) on DREAM Set3 indels (Wang et al. 2020)
assessed by: Select a tumour DNA somatic variant-calling workflow

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