R Package: annotated gene-level VCFs and ancestry-informed analyses from ClinVar data.
The goal of clinvaR is to quickly generate a VCF of annotated variants relevant to a list of genes, and produce simple, ancestry-informed analyses.
# install.packages("devtools")
devtools::install_github("jamesdiao/clinvaR")
require(clinvaR)To acquire a VCF with the July 5, 2017 ClinVar file and all default settings, simply run annotate(genes).
More specific modifications can be made by changing the 4 steps:
- Select a list of genes that you are interested in. This can be done by manual input, by importing a .tsv from MacArthur's gene lists (stored locally), or by importing your own .tsv file:
get_genes() - Download and import relevant variants from 1000 Genomes:
download_1000g(), import_file_1000g(). - Select a version of ClinVar. These can be downloaded directly:
download_clinvar(). Alternatively, ClinVar VCFs before July 2017 can be retrieved locally:get_clinvar(). - Use the ClinVar file to annotate the gene-level variant VCF:
annotate_1000g().
clinvaR also provides a few basic analysis and visualization functions that can be run directly : freq_over_time, var_plot_1000g.