GRAPE requires a 64-bit version of Linux.

Total amount of required disk space must be at least 50GB.


Download the latest release and extract it to your selected directory.

Alternatively, you can clone the most recent (unstable) version from the GitHub repository:

git clone

Build docker container from the GRAPE directory:

docker build -t grape:latest -f containers/snakemake/Dockerfile -m 8GB .

Download Reference Datasets

Reference datasets are required for correct pipeline operataion.

To download reference dataset one should use reference command of the pipeline launcher.

The command below downloads needed references to the directory specified by the flag –ref-directory. After that –ref-directory argument should be used in all subsequent commands.

docker run --rm -it -v /media:/media -v /etc/localtime:/etc/localtime:ro \
grape:latest reference --ref-directory /media/ref --real-run

If phasing and imputation are required (mainly for the GERMLINE workflow) one should specify additional –phase and –impute flags to previous command to download additional reference datasets.

docker run --rm -it -v /media:/media -v /etc/localtime:/etc/localtime:ro \
grape:latest reference \
    --ref-directory /media/ref --phase --impute --real-run

There are another options to download all required reference data as a single file. This file is prepared by the GRAPE developers and preloaded on our side in the cloud.

It can be done by specifying additional flag –use-bundle to the reference command. This way is faster, since all the post-processing procedures have been already performed.

docker run --rm -it -v /media:/media -v /etc/localtime:/etc/localtime:ro \
grape:latest reference --use-bundle \
    --ref-directory /media/ref --phase --impute --real-run


This step only needs to be done once.