VPMBench: a test bench for variant prioritization methods

VPMBench: a test bench for variant prioritization methods

Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed over the last years to aid clinicians in identifying variants that are likely disease-causi...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 22; no. Suppl 5; pp. 1 - 543
Main Authors: Ruscheinski, Andreas, Reimler, Anna Lena, Ewald, Roland, Uhrmacher, Adelinde M
Format: Journal Article
Language:English
Published: London BioMed Central Ltd 08-11-2021
BioMed Central
BMC
Subjects:
Algorithms
Analysis
Bioinformatics
Computational biology
DNA sequencing
Evaluation
Gene sequencing
Genetic diversity
Genetic variance
Genomes
Genomic structural variations
Identification and classification
Methods
Nucleotide sequencing
Pipelines
Software
Test bench
Test bias
Variant prioritization
Whole genome sequencing
Germany
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Summary:Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed over the last years to aid clinicians in identifying variants that are likely disease-causing. Each time a new method is developed, its effectiveness must be evaluated and compared to other approaches based on the most recently available evaluation data. Doing so in an unbiased, systematic, and replicable manner requires significant effort. The open-source test bench "VPMBench" automates the evaluation of variant prioritization methods. VPMBench introduces a standardized interface for prioritization methods and provides a plugin system that makes it easy to evaluate new methods. It supports different input data formats and custom output data preparation. VPMBench exploits declaratively specified information about the methods, e.g., the variants supported by the methods. Plugins may also be provided in a technology-agnostic manner via containerization. VPMBench significantly simplifies the evaluation of both custom and published variant prioritization methods. As we expect variant prioritization methods to become ever more critical with the advent of whole-genome sequencing in clinical diagnostics, such tool support is crucial to facilitate methodological research.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-021-04458-0