recipe bioconductor-structuralvariantannotation

Variant annotations for structural variants



GPL-3 + file LICENSE



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.

package bioconductor-structuralvariantannotation

(downloads) docker_bioconductor-structuralvariantannotation



depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends bioconductor-variantannotation:


depends r-assertthat:

depends r-base:


depends r-dplyr:

depends r-rlang:

depends r-stringr:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-structuralvariantannotation

and update with::

   mamba update bioconductor-structuralvariantannotation

To create a new environment, run:

mamba create --name myenvname bioconductor-structuralvariantannotation

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-structuralvariantannotation/tags`_ for valid values for ``<tag>``)

Download stats