Install

A ready-to-use Docker image is available to download here.

docker pull b3rse/granite:<version>

Run granite using Docker as follows:

docker run b3rse/granite:<version> granite <command> ...

If installed locally, additional software needs to be available in the environment to run certain commands:

• Samtools

• bgzip

• tabix

To install the program from source:

git clone https://github.com/dbmi-bgm/granite
cd granite
make configure && make build

To install the program with pip:

pip install granite-suite

VEP

The comHet command requires gene- and transcript-level annotations produced by the Ensembl Variant Effect Predictor (VEP). granite does not run VEP directly; instead, it consumes VEP annotations already present in the input VCF file and uses them to assign variants to genes and transcripts and to evaluate inheritance patterns.

VEP annotations are expected to follow the standard VCF INFO field format (e.g. the CSQ tag), as produced by default VEP configurations. For details on running VEP and generating compatible annotations, please refer to the official documentation: https://github.com/Ensembl/ensembl-vep