Configuration

MuSE v1.0rc (Wang et al. 2020)

MuSE as run in the cited comparison.

Overview

MuSE 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

8 evaluations · 32 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: MuSE v1.0rc (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	1650 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 MuSE 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', D79; dataset 'AML'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (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	0.786 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 MuSE 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', G79; dataset 'AML'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (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	0.713 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 MuSE 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', F79; dataset 'AML'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (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	0.876 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 MuSE 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', E79; dataset 'AML'; caller 'MuSE'; column 'Recall'
Configuration: MuSE v1.0rc (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	1890 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 MuSE 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', D64; dataset 'CLL'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (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	0.647 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 MuSE 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', G64; dataset 'CLL'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (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	0.549 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 MuSE 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', F64; dataset 'CLL'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (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	0.788 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 MuSE 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', E64; dataset 'CLL'; caller 'MuSE'; column 'Recall'
Configuration: MuSE v1.0rc (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	39000 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 MuSE 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', D109; dataset 'COLO'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (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	0.931 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 MuSE 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', G109; dataset 'COLO'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (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	0.89 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 MuSE 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', F109; dataset 'COLO'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (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	0.976 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 MuSE 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', E109; dataset 'COLO'; caller 'MuSE'; column 'Recall'
Configuration: MuSE v1.0rc (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)	4030 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 MuSE 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', D4; dataset 'DREAM Set1'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (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)	0.911 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 MuSE 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', G4; dataset 'DREAM Set1'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (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)	0.855 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 MuSE 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', F4; dataset 'DREAM Set1'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (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)	0.975 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 MuSE 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', E4; dataset 'DREAM Set1'; caller 'MuSE'; column 'Recall'
Configuration: MuSE v1.0rc (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)	4630 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 MuSE 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', D19; dataset 'DREAM Set2'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (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)	0.938 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 MuSE 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', G19; dataset 'DREAM Set2'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (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)	0.907 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 MuSE 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', F19; dataset 'DREAM Set2'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (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)	0.971 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 MuSE 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', E19; dataset 'DREAM Set2'; caller 'MuSE'; column 'Recall'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	7250 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 MuSE on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-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', D34; dataset 'DREAM Set3'; caller 'MuSE'; column 'Count'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.918 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 MuSE on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-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', G34; dataset 'DREAM Set3'; caller 'MuSE'; column 'F1'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.959 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 MuSE on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-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', F34; dataset 'DREAM Set3'; caller 'MuSE'; column 'Precision'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 3 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 3 (WGS)	0.88 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 MuSE on DREAM Set3 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set3-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', E34; dataset 'DREAM Set3'; caller 'MuSE'; column 'Recall'
Configuration: MuSE v1.0rc (Wang et al. 2020)	Protocol: DREAM synthetic set 4 somatic SNVs, WGS (Wang et al. 2020 Table S1) Dataset: ICGC-TCGA DREAM synthetic set 4 (WGS)	10300 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 MuSE on DREAM Set4 SNVs (Wang et al. 2020) somatic-20261009-protocol-wang2020-dream-set4-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', D49; dataset 'DREAM Set4'; caller 'MuSE'; 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-muse

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: MuSE
protocol: Option -G for WGS
foundation model eligible: false
source locator: Methods, Somatic variant calling paragraph 1 and 2; Table S1/S2 row label 'MuSE'
version: v1.0rc

Related records

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

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