Cpipe is a clinically focused exome sequencing pipeline developed by the Melbourne Genomics Health Alliance. Cpipe offers an industry standard variant calling pipeline with a suite of additional features needed by diagnostic laboratories added on top.
To set up Cpipe, clone this repository and then run the install script:
git clone https://github.com/MelbourneGenomics/cpipe.git
cd cpipe
./pipeline/scripts/install.sh
For further instructions, take a look at the User Guide.