Configuration

SomaticSniper v1.0.5.0 (Wang et al. 2020)

SomaticSniper as run in the cited comparison.

Overview

SomaticSniper 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: SomaticSniper v1.0.5.0 (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	51000 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 SomaticSniper 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', D83; dataset 'AML'; caller 'SomaticSniper'; column 'Count'
Configuration: SomaticSniper v1.0.5.0 (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	0.041 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 SomaticSniper 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', G83; dataset 'AML'; caller 'SomaticSniper'; column 'F1'
Configuration: SomaticSniper v1.0.5.0 (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	0.021 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 SomaticSniper 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', F83; dataset 'AML'; caller 'SomaticSniper'; column 'Precision'
Configuration: SomaticSniper v1.0.5.0 (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	0.803 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 SomaticSniper 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', E83; dataset 'AML'; caller 'SomaticSniper'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (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	7740 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 SomaticSniper 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', D68; dataset 'CLL'; caller 'SomaticSniper'; column 'Count'
Configuration: SomaticSniper v1.0.5.0 (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	0.253 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 SomaticSniper 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', G68; dataset 'CLL'; caller 'SomaticSniper'; column 'F1'
Configuration: SomaticSniper v1.0.5.0 (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	0.148 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 SomaticSniper 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', F68; dataset 'CLL'; caller 'SomaticSniper'; column 'Precision'
Configuration: SomaticSniper v1.0.5.0 (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	0.87 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 SomaticSniper 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', E68; dataset 'CLL'; caller 'SomaticSniper'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (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	75900 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 SomaticSniper 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', D113; dataset 'COLO'; caller 'SomaticSniper'; column 'Count'
Configuration: SomaticSniper v1.0.5.0 (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	0.287 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 SomaticSniper 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', G113; dataset 'COLO'; caller 'SomaticSniper'; column 'F1'
Configuration: SomaticSniper v1.0.5.0 (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	0.211 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 SomaticSniper 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', F113; dataset 'COLO'; caller 'SomaticSniper'; column 'Precision'
Configuration: SomaticSniper v1.0.5.0 (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	0.45 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 SomaticSniper 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', E113; dataset 'COLO'; caller 'SomaticSniper'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (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)	9030 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 SomaticSniper 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', D8; dataset 'DREAM Set1'; caller 'SomaticSniper'; column 'Count'
Configuration: SomaticSniper v1.0.5.0 (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)	0.55 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 SomaticSniper 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', G8; dataset 'DREAM Set1'; caller 'SomaticSniper'; column 'F1'
Configuration: SomaticSniper v1.0.5.0 (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)	0.383 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 SomaticSniper 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', F8; dataset 'DREAM Set1'; caller 'SomaticSniper'; column 'Precision'
Configuration: SomaticSniper v1.0.5.0 (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)	0.978 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 SomaticSniper 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', E8; dataset 'DREAM Set1'; caller 'SomaticSniper'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (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)	10200 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 SomaticSniper 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', D23; dataset 'DREAM Set2'; caller 'SomaticSniper'; column 'Count'
Configuration: SomaticSniper v1.0.5.0 (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)	0.581 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 SomaticSniper 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', G23; dataset 'DREAM Set2'; caller 'SomaticSniper'; column 'F1'
Configuration: SomaticSniper v1.0.5.0 (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)	0.414 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 SomaticSniper 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', F23; dataset 'DREAM Set2'; caller 'SomaticSniper'; column 'Precision'
Configuration: SomaticSniper v1.0.5.0 (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)	0.977 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 SomaticSniper 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', E23; dataset 'DREAM Set2'; caller 'SomaticSniper'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (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)	12200 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 SomaticSniper 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', D38; dataset 'DREAM Set3'; caller 'SomaticSniper'; column 'Count'
Configuration: SomaticSniper v1.0.5.0 (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)	0.667 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 SomaticSniper 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', G38; dataset 'DREAM Set3'; caller 'SomaticSniper'; column 'F1'
Configuration: SomaticSniper v1.0.5.0 (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)	0.549 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 SomaticSniper 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', F38; dataset 'DREAM Set3'; caller 'SomaticSniper'; column 'Precision'
Configuration: SomaticSniper v1.0.5.0 (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)	0.848 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 SomaticSniper 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', E38; dataset 'DREAM Set3'; caller 'SomaticSniper'; column 'Recall'
Configuration: SomaticSniper v1.0.5.0 (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)	16500 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 SomaticSniper 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', D53; dataset 'DREAM Set4'; caller 'SomaticSniper'; 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-somaticsniper

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: SomaticSniper
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 'SomaticSniper'
version: v1.0.5.0

Related records

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

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