Configuration

Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)

5callers (>=2) as run in the cited comparison.

Overview

5callers (>=2) as run in the cited comparison.

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

Evaluations and results

5 evaluations · 20 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: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: CLL tumour somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: Chronic lymphocytic leukaemia tumour-normal WGS with curated somatic calls	398 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on CLL indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-cll-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', D37; dataset 'CLL'; caller '5callers (>=2)'; column 'Count'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: CLL tumour somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: Chronic lymphocytic leukaemia tumour-normal WGS with curated somatic calls	0.342 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on CLL indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-cll-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', G37; dataset 'CLL'; caller '5callers (>=2)'; column 'F1'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: CLL tumour somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: Chronic lymphocytic leukaemia tumour-normal WGS with curated somatic calls	0.229 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on CLL indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-cll-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', F37; dataset 'CLL'; caller '5callers (>=2)'; column 'Precision'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: CLL tumour somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: Chronic lymphocytic leukaemia tumour-normal WGS with curated somatic calls	0.679 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on CLL indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-cll-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', E37; dataset 'CLL'; caller '5callers (>=2)'; column 'Recall'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: COLO829 cell line somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: COLO829 metastatic melanoma cell line tumour-normal WGS with curated somatic calls	1600 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on COLO indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-colo829-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', D61; dataset 'COLO'; caller '5callers (>=2)'; column 'Count'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: COLO829 cell line somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: COLO829 metastatic melanoma cell line tumour-normal WGS with curated somatic calls	0.381 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on COLO indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-colo829-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', G61; dataset 'COLO'; caller '5callers (>=2)'; column 'F1'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: COLO829 cell line somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: COLO829 metastatic melanoma cell line tumour-normal WGS with curated somatic calls	0.244 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on COLO indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-colo829-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', F61; dataset 'COLO'; caller '5callers (>=2)'; column 'Precision'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: COLO829 cell line somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: COLO829 metastatic melanoma cell line tumour-normal WGS with curated somatic calls	0.872 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on COLO indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-colo829-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', E61; dataset 'COLO'; caller '5callers (>=2)'; column 'Recall'
Configuration: Majority vote, 5 indel callers, at least 2 agree (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)	6030 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) 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', D13; dataset 'DREAM Set3'; caller '5callers (>=2)'; column 'Count'
Configuration: Majority vote, 5 indel callers, at least 2 agree (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)	0.817 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) 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', G13; dataset 'DREAM Set3'; caller '5callers (>=2)'; column 'F1'
Configuration: Majority vote, 5 indel callers, at least 2 agree (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)	0.95 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) 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', F13; dataset 'DREAM Set3'; caller '5callers (>=2)'; column 'Precision'
Configuration: Majority vote, 5 indel callers, at least 2 agree (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)	0.717 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) 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', E13; dataset 'DREAM Set3'; caller '5callers (>=2)'; column 'Recall'
Configuration: Majority vote, 5 indel callers, at least 2 agree (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)	11000 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) 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', D25; dataset 'DREAM Set4'; caller '5callers (>=2)'; column 'Count'
Configuration: Majority vote, 5 indel callers, at least 2 agree (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)	0.846 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) 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', G25; dataset 'DREAM Set4'; caller '5callers (>=2)'; column 'F1'
Configuration: Majority vote, 5 indel callers, at least 2 agree (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)	0.969 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) 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', F25; dataset 'DREAM Set4'; caller '5callers (>=2)'; column 'Precision'
Configuration: Majority vote, 5 indel callers, at least 2 agree (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)	0.75 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) 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', E25; dataset 'DREAM Set4'; caller '5callers (>=2)'; column 'Recall'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: MB brain tumour somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: Malignant paediatric cerebellar brain tumour (MB) tumour-normal WGS with curated somatic calls	975 count count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on MB indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-mb-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', D49; dataset 'MB'; caller '5callers (>=2)'; column 'Count'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: MB brain tumour somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: Malignant paediatric cerebellar brain tumour (MB) tumour-normal WGS with curated somatic calls	0.507 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on MB indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-mb-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', G49; dataset 'MB'; caller '5callers (>=2)'; column 'F1'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: MB brain tumour somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: Malignant paediatric cerebellar brain tumour (MB) tumour-normal WGS with curated somatic calls	0.344 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on MB indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-mb-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', F49; dataset 'MB'; caller '5callers (>=2)'; column 'Precision'
Configuration: Majority vote, 5 indel callers, at least 2 agree (Wang et al. 2020)	Protocol: MB brain tumour somatic indels, WGS (Wang et al. 2020 Table S2) Dataset: Malignant paediatric cerebellar brain tumour (MB) tumour-normal WGS with curated somatic calls	0.965 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5callers (>=2) on MB indels (Wang et al. 2020) somatic-20261009-protocol-wang2020-mb-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', E49; dataset 'MB'; caller '5callers (>=2)'; column 'Recall'

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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-config-wang2020-vote-5callers-min2

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: 5callers (>=2)
protocol: Voting over LoFreq, MuTect2, Strelka, VarDict and VarScan; a call needs at least 2 callers
foundation model eligible: false
source locator: Methods, Somatic variant calling paragraph 1 and 2; Table S1/S2 row label '5callers (>=2)'
method role: Authors' own consensus approach evaluated alongside the individual callers
missing metadata: version: reason: inapplicable; note: Ensemble of the listed caller versions; no separate version

Related records

configuration of: Majority-vote consensus of somatic callers
system: 5callers (>=2) on CLL indels (Wang et al. 2020)
system: 5callers (>=2) on COLO indels (Wang et al. 2020)
system: 5callers (>=2) on DREAM Set3 indels (Wang et al. 2020)
system: 5callers (>=2) on DREAM Set4 indels (Wang et al. 2020)
system: 5callers (>=2) on MB indels (Wang et al. 2020)

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