Configuration

Union of 3 indel callers (at least 1) (Wang et al. 2020)

3callers (>=1) as run in the cited comparison.

Overview

3callers (>=1) 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: Union of 3 indel callers (at least 1) (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	1360 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 (>=1) 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', D35; dataset 'CLL'; caller '3callers (>=1)'; column 'Count'
Configuration: Union of 3 indel callers (at least 1) (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	0.127 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 (>=1) 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', G35; dataset 'CLL'; caller '3callers (>=1)'; column 'F1'
Configuration: Union of 3 indel callers (at least 1) (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	0.07 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 (>=1) 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', F35; dataset 'CLL'; caller '3callers (>=1)'; column 'Precision'
Configuration: Union of 3 indel callers (at least 1) (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	0.709 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 (>=1) 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', E35; dataset 'CLL'; caller '3callers (>=1)'; column 'Recall'
Configuration: Union of 3 indel callers (at least 1) (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	3350 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 (>=1) 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', D59; dataset 'COLO'; caller '3callers (>=1)'; column 'Count'
Configuration: Union of 3 indel callers (at least 1) (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	0.21 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 (>=1) 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', G59; dataset 'COLO'; caller '3callers (>=1)'; column 'F1'
Configuration: Union of 3 indel callers (at least 1) (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	0.119 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 (>=1) 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', F59; dataset 'COLO'; caller '3callers (>=1)'; column 'Precision'
Configuration: Union of 3 indel callers (at least 1) (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	0.895 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 (>=1) 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', E59; dataset 'COLO'; caller '3callers (>=1)'; column 'Recall'
Configuration: Union of 3 indel callers (at least 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)	6800 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 (>=1) 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', D11; dataset 'DREAM Set3'; caller '3callers (>=1)'; column 'Count'
Configuration: Union of 3 indel callers (at least 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)	0.791 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 (>=1) 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', G11; dataset 'DREAM Set3'; caller '3callers (>=1)'; column 'F1'
Configuration: Union of 3 indel callers (at least 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)	0.86 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 (>=1) 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', F11; dataset 'DREAM Set3'; caller '3callers (>=1)'; column 'Precision'
Configuration: Union of 3 indel callers (at least 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)	0.732 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 (>=1) 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', E11; dataset 'DREAM Set3'; caller '3callers (>=1)'; column 'Recall'
Configuration: Union of 3 indel callers (at least 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)	12500 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 (>=1) 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', D23; dataset 'DREAM Set4'; caller '3callers (>=1)'; column 'Count'
Configuration: Union of 3 indel callers (at least 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)	0.846 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 3callers (>=1) 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', G23; dataset 'DREAM Set4'; caller '3callers (>=1)'; column 'F1'
Configuration: Union of 3 indel callers (at least 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)	0.903 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 (>=1) 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', F23; dataset 'DREAM Set4'; caller '3callers (>=1)'; column 'Precision'
Configuration: Union of 3 indel callers (at least 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)	0.795 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 (>=1) 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', E23; dataset 'DREAM Set4'; caller '3callers (>=1)'; column 'Recall'
Configuration: Union of 3 indel callers (at least 1) (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	10700 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 (>=1) 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', D47; dataset 'MB'; caller '3callers (>=1)'; column 'Count'
Configuration: Union of 3 indel callers (at least 1) (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	0.062 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 (>=1) 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', G47; dataset 'MB'; caller '3callers (>=1)'; column 'F1'
Configuration: Union of 3 indel callers (at least 1) (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	0.032 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 (>=1) 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', F47; dataset 'MB'; caller '3callers (>=1)'; column 'Precision'
Configuration: Union of 3 indel callers (at least 1) (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	0.983 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 (>=1) 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', E47; dataset 'MB'; caller '3callers (>=1)'; 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-min1

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: 3callers (>=1)
protocol: Voting over LoFreq, MuTect2 and Strelka; a call needs at least 1 caller
foundation model eligible: false
source locator: Methods, Somatic variant calling paragraph 1 and 2; Table S1/S2 row label '3callers (>=1)'
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 (>=1) on CLL indels (Wang et al. 2020)
system: 3callers (>=1) on COLO indels (Wang et al. 2020)
system: 3callers (>=1) on DREAM Set3 indels (Wang et al. 2020)
system: 3callers (>=1) on DREAM Set4 indels (Wang et al. 2020)
system: 3callers (>=1) on MB indels (Wang et al. 2020)

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