GEMSCAN

Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.

View the Project on GitHub NCI-CGR/GEMSCAN

Installation

The installation procese for the GEMSCAN pipeline is as follows:

Install a Conda-based Python3 distribution or activate conda
If needed, install git
Clone the GEMSCAN repository
Navigate into the repository directory
Follow the instruction here to to install the snakemake conda environment