Configuration

Majority vote, 3 indel callers, at least 2 agree (Wang et al. 2020)

3callers (>=2) as run in the cited comparison.

Overview

3callers (>=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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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Majority vote, 3 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	135 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 3callers (>=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', D34; dataset 'CLL'; caller '3callers (>=2)'; column 'Count'
Configuration: Majority vote, 3 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	0.513 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 3callers (>=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', G34; dataset 'CLL'; caller '3callers (>=2)'; column 'F1'
Configuration: Majority vote, 3 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	0.511 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 3callers (>=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', F34; dataset 'CLL'; caller '3callers (>=2)'; column 'Precision'
Configuration: Majority vote, 3 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	0.515 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 3callers (>=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', E34; dataset 'CLL'; caller '3callers (>=2)'; column 'Recall'
Configuration: Majority vote, 3 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	730 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 3callers (>=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', D58; dataset 'COLO'; caller '3callers (>=2)'; column 'Count'
Configuration: Majority vote, 3 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	0.607 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 3callers (>=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', G58; dataset 'COLO'; caller '3callers (>=2)'; column 'F1'
Configuration: Majority vote, 3 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	0.489 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 3callers (>=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', F58; dataset 'COLO'; caller '3callers (>=2)'; column 'Precision'
Configuration: Majority vote, 3 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	0.8 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 3callers (>=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', E58; dataset 'COLO'; caller '3callers (>=2)'; column 'Recall'
Configuration: Majority vote, 3 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)	5410 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 3callers (>=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', D10; dataset 'DREAM Set3'; caller '3callers (>=2)'; column 'Count'
Configuration: Majority vote, 3 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)	0.803 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 3callers (>=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', G10; dataset 'DREAM Set3'; caller '3callers (>=2)'; column 'F1'
Configuration: Majority vote, 3 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)	0.995 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 3callers (>=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', F10; dataset 'DREAM Set3'; caller '3callers (>=2)'; column 'Precision'
Configuration: Majority vote, 3 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)	0.673 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 3callers (>=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', E10; dataset 'DREAM Set3'; caller '3callers (>=2)'; column 'Recall'
Configuration: Majority vote, 3 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)	8450 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 3callers (>=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', D22; dataset 'DREAM Set4'; caller '3callers (>=2)'; column 'Count'
Configuration: Majority vote, 3 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)	0.741 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 3callers (>=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', G22; dataset 'DREAM Set4'; caller '3callers (>=2)'; column 'F1'
Configuration: Majority vote, 3 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)	0.993 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 3callers (>=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', F22; dataset 'DREAM Set4'; caller '3callers (>=2)'; column 'Precision'
Configuration: Majority vote, 3 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)	0.591 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 3callers (>=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', E22; dataset 'DREAM Set4'; caller '3callers (>=2)'; column 'Recall'
Configuration: Majority vote, 3 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	616 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 3callers (>=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', D46; dataset 'MB'; caller '3callers (>=2)'; column 'Count'
Configuration: Majority vote, 3 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	0.544 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 3callers (>=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', G46; dataset 'MB'; caller '3callers (>=2)'; column 'F1'
Configuration: Majority vote, 3 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	0.425 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 3callers (>=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', F46; dataset 'MB'; caller '3callers (>=2)'; column 'Precision'
Configuration: Majority vote, 3 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	0.755 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 3callers (>=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', E46; dataset 'MB'; caller '3callers (>=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-3callers-min2

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: 3callers (>=2)
protocol: Majority voting over LoFreq, MuTect2 and Strelka; 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 '3callers (>=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: 3callers (>=2) on CLL indels (Wang et al. 2020)
system: 3callers (>=2) on COLO indels (Wang et al. 2020)
system: 3callers (>=2) on DREAM Set3 indels (Wang et al. 2020)
system: 3callers (>=2) on DREAM Set4 indels (Wang et al. 2020)
system: 3callers (>=2) on MB indels (Wang et al. 2020)

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