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Variant annotations for structural variants

Bioconductor version: Release (3.19)

StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Author: Daniel Cameron [aut, cre] , Ruining Dong [aut]

Maintainer: Daniel Cameron <daniel.l.cameron at>

Citation (from within R, enter citation("StructuralVariantAnnotation")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Structural Variant Annotation Package HTML R Script
Reference Manual PDF


biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-3 + file LICENSE
Depends GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0)
Imports assertthat, Biostrings, pwalign, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb
System Requirements
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Suggests ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19
Linking To
Depends On Me svaNUMT, svaRetro
Imports Me
Suggests Me shiny.gosling
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package StructuralVariantAnnotation_1.20.0.tar.gz
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macOS Binary (x86_64) StructuralVariantAnnotation_1.20.0.tgz
macOS Binary (arm64) StructuralVariantAnnotation_1.20.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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