Simple combination of multiple somatic variant callers to increase accuracy

Publications comparing variant caller algorithms present discordant results with contradictory rankings. Caller performances are inconsistent and wide ranging, and dependent upon input data, application, parameter settings, and evaluation metric. With no single variant caller emerging as a superior...

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Bibliographic Details
Published in:Scientific reports 2023-05, Vol.13 (1), p.8463-8463, Article 8463
Main Authors: Trevarton, Alexander J., Chang, Jeffrey T., Symmans, W. Fraser
Format: Article
Language:English
Subjects:
631/67/1347
631/67/69
Accuracy
Algorithms
Datasets
Exome - genetics
Genome, Human
Genomes
High-Throughput Nucleotide Sequencing - methods
Humanities and Social Sciences
Humans
multidisciplinary
Neoplasms - genetics
Noise reduction
Polymorphism, Single Nucleotide
Science
Science (multidisciplinary)
Software
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Summary:Publications comparing variant caller algorithms present discordant results with contradictory rankings. Caller performances are inconsistent and wide ranging, and dependent upon input data, application, parameter settings, and evaluation metric. With no single variant caller emerging as a superior standard, combinations or ensembles of variant callers have appeared in the literature. In this study, a whole genome somatic reference standard was used to derive principles to guide strategies for combining variant calls. Then, manually annotated variants called from the whole exome sequencing of a tumor were used to corroborate these general principles. Finally, we examined the ability of these principles to reduce noise in targeted sequencing.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-023-34925-y