StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem
- Author(s)
- Cameron, DL; Dong, R; Papenfuss, AT;
- Details
- Publication Year 2022-03-28,Volume 38,Issue #7,Page 2046-2048
- Journal Title
- Bioinformatics
- Abstract
- SUMMARY: StructuralVariantAnnotation is an R/Bioconductor package that provides a framework for decoupling downstream analysis of structural variant breakpoints from upstream variant calling methods. It standardizes the representational format from BEDPE, or any of the three different notations supported by VCF into a breakpoint GRanges data structure suitable for use by the wider Bioconductor ecosystem. It handles both transitive breakpoints and duplication/insertion notational differences of identical variants-both common scenarios when comparing short/long read-based call sets that confound downstream analysis. StructuralVariantAnnotation provides the caller-agnostic foundation needed for a R/Bioconductor ecosystem of structural variant annotation, classification and interpretation tools able to handle both simple and complex genomic rearrangements. AVAILABILITY AND IMPLEMENTATION: StructuralVariantAnnotation is implemented in R and available for download as the Bioconductor StructuralVariantAnnotation package. Details can be found at https://www.bioconductor.org/packages/release/bioc/html/StructuralVariantAnnotation.html. It has been released under a GPL license.
- Keywords
- Ecosystem; Software; Genomics/methods; Genome
- Research Division(s)
- Bioinformatics
- PubMed ID
- 35134827
- Publisher's Version
- https://doi.org/10.1093/bioinformatics/btac042
- Open Access at Publisher's Site
https://doi.org/10.1093/bioinformatics/btac042- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
- Documents
Creation Date: 2023-02-24 09:21:02
Last Modified: 2023-02-24 09:24:45