The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline
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batches Initial checking of Cpipe code Apr 2, 2015
pipeline update default config values to match current software set Feb 26, 2016
tmpdata Set tmp directory to a location inside Cpipe directory by default, to… May 17, 2015
tools add missing updated version of groovy-ngs-utils jar Jul 19, 2015
.gitignore gene list management functionality Oct 9, 2015
GPLv3.txt Added main GPL license and license file specifying additional terms Apr 13, 2015
bpipe unset GROOVY_HOME in case the user has already set that variable May 5, 2015


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
cd cpipe

For further instructions, take a look at the User Guide.