AnVILVRS

The AnVILVRS R package provides tools to work with genomic variation data, leveraging the GA4GH Variant Representation Specification (VRS). It serves as an R interface to the vrs_anvil_toolkit Python package, allowing users to translate variant identifiers into VRS seamlessly within the R environment.

Installation

First, install the AnVILVRS package from GitHub:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("Bioconductor/AnVILVRS")

Next, set up the necessary Python environment. The package provides a function to handle the installation of the required Python dependencies in a reticulate virtual environment.

library(AnVILVRS)
install_AnVILVRS()

This will create a Python virtual environment named vrs_env and install all the necessary components.

Usage

Before using the package functions, load the virtual environment:

library(reticulate)
use_virtualenv("vrs_env", required = TRUE)

Here is an example of how to translate a variant in gnomAD format to a VRS Allele ID:

library(AnVILVRS)
# Translate a gnomad variant to a VRS ID
get_vrs_id("chr7-87509329-A-G", "gnomad")

The package also supports other formats like spdi, hgvs, and beacon.

For more information on the available functions, please refer to the package documentation.