Configuration

LoFreq v2.1.3.1 (Wang et al. 2020)

LoFreq as run in the cited comparison.

Overview

LoFreq 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: LoFreq v2.1.3.1 (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	1710 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 LoFreq 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', D82; dataset 'AML'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (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	0.745 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 LoFreq 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', G82; dataset 'AML'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (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	0.664 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 LoFreq 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', F82; dataset 'AML'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (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	0.848 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 LoFreq 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', E82; dataset 'AML'; caller 'LoFreq'; column 'Recall'
Configuration: LoFreq v2.1.3.1 (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	758 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 LoFreq 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', D30; dataset 'CLL'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (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	0.126 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 LoFreq 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', G30; dataset 'CLL'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (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	0.0739 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 LoFreq 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', F30; dataset 'CLL'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (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	0.418 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 LoFreq 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', E30; dataset 'CLL'; caller 'LoFreq'; column 'Recall'
Configuration: LoFreq v2.1.3.1 (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	1230 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 LoFreq 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', D67; dataset 'CLL'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (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	0.702 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 LoFreq 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', G67; dataset 'CLL'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (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	0.728 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 LoFreq 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', F67; dataset 'CLL'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (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	0.678 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 LoFreq 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', E67; dataset 'CLL'; caller 'LoFreq'; column 'Recall'
Configuration: LoFreq v2.1.3.1 (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	1660 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 LoFreq 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', D54; dataset 'COLO'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (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	0.322 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 LoFreq 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', G54; dataset 'COLO'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (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	0.204 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 LoFreq 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', F54; dataset 'COLO'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (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	0.76 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 LoFreq 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', E54; dataset 'COLO'; caller 'LoFreq'; column 'Recall'
Configuration: LoFreq v2.1.3.1 (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	37400 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 LoFreq 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', D112; dataset 'COLO'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (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 LoFreq 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', G112; dataset 'COLO'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (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	0.908 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 LoFreq 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', F112; dataset 'COLO'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (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	0.955 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 LoFreq 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', E112; dataset 'COLO'; caller 'LoFreq'; column 'Recall'
Configuration: LoFreq v2.1.3.1 (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)	3480 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 LoFreq 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', D7; dataset 'DREAM Set1'; caller 'LoFreq'; column 'Count'
Configuration: LoFreq v2.1.3.1 (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)	0.963 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 LoFreq 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', G7; dataset 'DREAM Set1'; caller 'LoFreq'; column 'F1'
Configuration: LoFreq v2.1.3.1 (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)	0.97 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 LoFreq 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', F7; dataset 'DREAM Set1'; caller 'LoFreq'; column 'Precision'
Configuration: LoFreq v2.1.3.1 (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)	0.956 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 LoFreq 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', E7; dataset 'DREAM Set1'; caller 'LoFreq'; column 'Recall'
Configuration: LoFreq v2.1.3.1 (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)	4190 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 LoFreq 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', D22; dataset 'DREAM Set2'; caller 'LoFreq'; column 'Count'

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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-lofreq

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: LoFreq
protocol: Default settings or author instructions
foundation model eligible: false
source locator: Methods, Somatic variant calling paragraph 1 and 2; Table S1/S2 row label 'LoFreq'
version: v2.1.3.1

Related records

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

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