- Clone the reposirotory:
git clone https://github.com/NotAPoetButACriminal/varwolf.git
- Navigate to the cloned directory and build the docker image:
docker build -t varwolf:latest .
- Run the database install script which will download the hg38 reference genome and all the necessary annotation files:
docker run --rm -itv /path/to/varwolf/:/root/varwolf/ varwolf:latest database_install
varannosaur is the script for annotating variants files using Ensembl VEP. Place a vcf file anywhere in the varwolf directory (such as the input/ directory), and run the following command:
docker run --rm -v /path/to/varwolf/:/root/varwolf varwolf:latest varannosaur input/variants.vcf(.gz)
The result is a table of annotated variants in tab-delimited format that is stored in the output/ directory and will have the name "*_annotated.tsv"