Configuration

VarScan v2.3.9 (Wang et al. 2020)

VarScan as run in the cited comparison.

Overview

VarScan 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: VarScan v2.3.9 (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	4360 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 VarScan 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', D85; dataset 'AML'; caller 'VarScan'; column 'Count'
Configuration: VarScan v2.3.9 (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	0.374 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 VarScan 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', G85; dataset 'AML'; caller 'VarScan'; column 'F1'
Configuration: VarScan v2.3.9 (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	0.245 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 VarScan 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', F85; dataset 'AML'; caller 'VarScan'; column 'Precision'
Configuration: VarScan v2.3.9 (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	0.795 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 VarScan 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', E85; dataset 'AML'; caller 'VarScan'; column 'Recall'
Configuration: VarScan v2.3.9 (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	2720 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 VarScan 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', D32; dataset 'CLL'; caller 'VarScan'; column 'Count'
Configuration: VarScan v2.3.9 (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	0.0602 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 VarScan 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', G32; dataset 'CLL'; caller 'VarScan'; column 'F1'
Configuration: VarScan v2.3.9 (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	0.0316 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 VarScan 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', F32; dataset 'CLL'; caller 'VarScan'; column 'Precision'
Configuration: VarScan v2.3.9 (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	0.642 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 VarScan 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', E32; dataset 'CLL'; caller 'VarScan'; column 'Recall'
Configuration: VarScan v2.3.9 (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	6250 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 VarScan 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', D70; dataset 'CLL'; caller 'VarScan'; column 'Count'
Configuration: VarScan v2.3.9 (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	0.294 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 VarScan 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', G70; dataset 'CLL'; caller 'VarScan'; column 'F1'
Configuration: VarScan v2.3.9 (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	0.178 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 VarScan 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', F70; dataset 'CLL'; caller 'VarScan'; column 'Precision'
Configuration: VarScan v2.3.9 (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	0.845 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 VarScan 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', E70; dataset 'CLL'; caller 'VarScan'; column 'Recall'
Configuration: VarScan v2.3.9 (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	4720 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 VarScan 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', D56; dataset 'COLO'; caller 'VarScan'; column 'Count'
Configuration: VarScan v2.3.9 (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	0.13 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 VarScan 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', G56; dataset 'COLO'; caller 'VarScan'; column 'F1'
Configuration: VarScan v2.3.9 (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	0.0714 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 VarScan 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', F56; dataset 'COLO'; caller 'VarScan'; column 'Precision'
Configuration: VarScan v2.3.9 (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	0.756 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 VarScan 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', E56; dataset 'COLO'; caller 'VarScan'; column 'Recall'
Configuration: VarScan v2.3.9 (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	42600 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 VarScan 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', D115; dataset 'COLO'; caller 'VarScan'; column 'Count'
Configuration: VarScan v2.3.9 (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	0.878 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 VarScan 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', G115; dataset 'COLO'; caller 'VarScan'; column 'F1'
Configuration: VarScan v2.3.9 (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	0.805 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 VarScan 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', F115; dataset 'COLO'; caller 'VarScan'; column 'Precision'
Configuration: VarScan v2.3.9 (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	0.966 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 VarScan 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', E115; dataset 'COLO'; caller 'VarScan'; column 'Recall'
Configuration: VarScan v2.3.9 (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)	7620 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 VarScan 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', D10; dataset 'DREAM Set1'; caller 'VarScan'; column 'Count'
Configuration: VarScan v2.3.9 (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)	0.622 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 VarScan 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', G10; dataset 'DREAM Set1'; caller 'VarScan'; column 'F1'
Configuration: VarScan v2.3.9 (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)	0.455 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 VarScan 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', F10; dataset 'DREAM Set1'; caller 'VarScan'; column 'Precision'
Configuration: VarScan v2.3.9 (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)	0.981 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 VarScan 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', E10; dataset 'DREAM Set1'; caller 'VarScan'; column 'Recall'
Configuration: VarScan v2.3.9 (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)	7990 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 VarScan 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', D25; dataset 'DREAM Set2'; caller 'VarScan'; 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-varscan

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: VarScan
protocol: Somatic calling with the somatic post-processing steps
foundation model eligible: false
source locator: Methods, Somatic variant calling paragraph 1 and 2; Table S1/S2 row label 'VarScan'
version: v2.3.9

Related records

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

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