Protocol

DREAM synthetic set 4 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 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	7530 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D18; dataset 'DREAM Set4'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.661 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G18; dataset 'DREAM Set4'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.954 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F18; dataset 'DREAM Set4'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.506 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E18; dataset 'DREAM Set4'; caller 'LoFreq'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	10900 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D21; dataset 'DREAM Set4'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.855 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G21; dataset 'DREAM Set4'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.985 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F21; dataset 'DREAM Set4'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E21; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	15000 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D27; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.84 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G27; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.818 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F27; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.864 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E27; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (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_Pass on DREAM Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D26; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.853 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G26; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.898 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F26; 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 indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.813 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 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E26; dataset 'DREAM Set4'; caller 'NeuSomatic_Pass'; column 'Recall'
Configuration: Strelka v2.7.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	8330 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 Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D19; dataset 'DREAM Set4'; caller 'Strelka'; column 'Count'
Configuration: Strelka v2.7.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) 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 Strelka on DREAM Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G19; dataset 'DREAM Set4'; caller 'Strelka'; column 'F1'
Configuration: Strelka v2.7.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.91 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 Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F19; dataset 'DREAM Set4'; caller 'Strelka'; column 'Precision'
Configuration: Strelka v2.7.1 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.534 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 Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E19; dataset 'DREAM Set4'; caller 'Strelka'; column 'Recall'
Configuration: VarDict through bcbio-nextgen v1.1.5 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	14500 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 Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D16; dataset 'DREAM Set4'; caller 'VarDict (bcbio)'; column 'Count'
Configuration: VarDict through bcbio-nextgen v1.1.5 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.762 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 Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', G16; dataset 'DREAM Set4'; caller 'VarDict (bcbio)'; column 'F1'
Configuration: VarDict through bcbio-nextgen v1.1.5 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.753 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 Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', F16; dataset 'DREAM Set4'; caller 'VarDict (bcbio)'; column 'Precision'
Configuration: VarDict through bcbio-nextgen v1.1.5 (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	0.771 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 Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', E16; dataset 'DREAM Set4'; caller 'VarDict (bcbio)'; column 'Recall'
Configuration: VarDict v1.6.0 standalone (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	60200 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 Set4 indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D17; dataset 'DREAM Set4'; 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-set4-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 Set4'
metric implementation: evaluator.py from Sage-Bionetworks/ICGC-TCGA-DREAM-Mutation-Calling-challenge-tools (commit not stated)
denominator: 14230
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 'S2 WGS INDELs', 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 indels (Wang et al. 2020)
assessment: MuTect2 on DREAM Set4 indels (Wang et al. 2020)
assessment: NeuSomatic_Lowqual on DREAM Set4 indels (Wang et al. 2020)
assessment: NeuSomatic_Pass on DREAM Set4 indels (Wang et al. 2020)
assessment: Strelka on DREAM Set4 indels (Wang et al. 2020)
assessment: VarDict (bcbio) on DREAM Set4 indels (Wang et al. 2020)
assessment: VarDict (standalone) on DREAM Set4 indels (Wang et al. 2020)
assessment: VarScan on DREAM Set4 indels (Wang et al. 2020)
assessment: 3callers (>=1) on DREAM Set4 indels (Wang et al. 2020)
assessment: 3callers (>=2) on DREAM Set4 indels (Wang et al. 2020)
assessment: 5callers (>=2) on DREAM Set4 indels (Wang et al. 2020)
assessment: 5callers (>=3) on DREAM Set4 indels (Wang et al. 2020)
assessed by: Select a tumour DNA somatic variant-calling workflow

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