StructuralVariantAnnotation 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.
The StructuralVariantAnnotation package can be installed using BioConductor:
if (!requireNamespace("BiocManager", quietly=TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("StructuralVariantAnnotation")