Configuration

MuTect2 (GATK v3.7-0) (Wang et al. 2020)

MuTect2 as run in the cited comparison.

Overview

MuTect2 as run in the cited comparison.

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Evaluations and results

13 evaluations · 52 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: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: AML tumour somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: Acute myeloid leukaemia tumour-normal WGS with platinum somatic list	7930 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 AML SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-aml-snv 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 'S1 WGS SNVs', D87; dataset 'AML'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: AML tumour somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: Acute myeloid leukaemia tumour-normal WGS with platinum somatic list	0.268 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 AML SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-aml-snv 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 'S1 WGS SNVs', G87; dataset 'AML'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: AML tumour somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: Acute myeloid leukaemia tumour-normal WGS with platinum somatic list	0.157 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 AML SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-aml-snv 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 'S1 WGS SNVs', F87; dataset 'AML'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: AML tumour somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: Acute myeloid leukaemia tumour-normal WGS with platinum somatic list	0.927 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 AML SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-aml-snv 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 'S1 WGS SNVs', E87; dataset 'AML'; caller 'MuTect2'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (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	267 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 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', D33; dataset 'CLL'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (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	0.279 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 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', G33; dataset 'CLL'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (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	0.21 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 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', F33; dataset 'CLL'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (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	0.418 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 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', E33; dataset 'CLL'; caller 'MuTect2'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: CLL tumour somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: Chronic lymphocytic leukaemia tumour-normal WGS with curated somatic calls	2940 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 CLL SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-cll-snv 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 'S1 WGS SNVs', D72; dataset 'CLL'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: CLL tumour somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: Chronic lymphocytic leukaemia tumour-normal WGS with curated somatic calls	0.523 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 CLL SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-cll-snv 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 'S1 WGS SNVs', G72; dataset 'CLL'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: CLL tumour somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: Chronic lymphocytic leukaemia tumour-normal WGS with curated somatic calls	0.379 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 CLL SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-cll-snv 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 'S1 WGS SNVs', F72; dataset 'CLL'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: CLL tumour somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: Chronic lymphocytic leukaemia tumour-normal WGS with curated somatic calls	0.847 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 CLL SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-cll-snv 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 'S1 WGS SNVs', E72; dataset 'CLL'; caller 'MuTect2'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (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	678 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 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', D57; dataset 'COLO'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (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	0.553 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 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', G57; dataset 'COLO'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (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	0.459 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 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', F57; dataset 'COLO'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (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	0.697 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 MuTect2 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', E57; dataset 'COLO'; caller 'MuTect2'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: COLO829 cell line somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: COLO829 metastatic melanoma cell line tumour-normal WGS with curated somatic calls	39300 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 COLO SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-colo829-snv 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 'S1 WGS SNVs', D117; dataset 'COLO'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: COLO829 cell line somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: COLO829 metastatic melanoma cell line tumour-normal WGS with curated somatic calls	0.886 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 COLO SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-colo829-snv 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 'S1 WGS SNVs', G117; dataset 'COLO'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: COLO829 cell line somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: COLO829 metastatic melanoma cell line tumour-normal WGS with curated somatic calls	0.843 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 COLO SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-colo829-snv 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 'S1 WGS SNVs', F117; dataset 'COLO'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: COLO829 cell line somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: COLO829 metastatic melanoma cell line tumour-normal WGS with curated somatic calls	0.933 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 COLO SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-colo829-snv 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 'S1 WGS SNVs', E117; dataset 'COLO'; caller 'MuTect2'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 1 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 1 (WGS)	4420 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 Set1 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set1-snv 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 'S1 WGS SNVs', D12; dataset 'DREAM Set1'; caller 'MuTect2'; column 'Count'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 1 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 1 (WGS)	0.87 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 Set1 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set1-snv 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 'S1 WGS SNVs', G12; dataset 'DREAM Set1'; caller 'MuTect2'; column 'F1'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 1 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 1 (WGS)	0.783 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 Set1 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set1-snv 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 'S1 WGS SNVs', F12; dataset 'DREAM Set1'; caller 'MuTect2'; column 'Precision'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 1 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 1 (WGS)	0.979 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 Set1 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set1-snv 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 'S1 WGS SNVs', E12; dataset 'DREAM Set1'; caller 'MuTect2'; column 'Recall'
Configuration: MuTect2 (GATK v3.7-0) (Wang et al. 2020)	Protocol: DREAM synthetic set 2 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 2 (WGS)	6080 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 Set2 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set2-snv 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 'S1 WGS SNVs', D27; dataset 'DREAM Set2'; caller 'MuTect2'; column 'Count'

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2 source records and release history

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-mutect2-gatk3-7

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: MuTect2
protocol: dbSNP v138 and COSMIC v80 supplied for WGS
foundation model eligible: false
source locator: Methods, Somatic variant calling paragraph 1 and 2; Table S1/S2 row label 'MuTect2'
version: GATK v3.7-0

Related records

configuration of: Mutect2
system: MuTect2 on AML SNVs (Wang et al. 2020)
system: MuTect2 on CLL indels (Wang et al. 2020)
system: MuTect2 on CLL SNVs (Wang et al. 2020)
system: MuTect2 on COLO indels (Wang et al. 2020)
system: MuTect2 on COLO SNVs (Wang et al. 2020)
system: MuTect2 on DREAM Set1 SNVs (Wang et al. 2020)
system: MuTect2 on DREAM Set2 SNVs (Wang et al. 2020)
system: MuTect2 on DREAM Set3 indels (Wang et al. 2020)
system: MuTect2 on DREAM Set3 SNVs (Wang et al. 2020)
system: MuTect2 on DREAM Set4 indels (Wang et al. 2020)
system: MuTect2 on DREAM Set4 SNVs (Wang et al. 2020)
system: MuTect2 on MB indels (Wang et al. 2020)
system: MuTect2 on MB SNVs (Wang et al. 2020)

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