This bundle package contains all materials necessary to run the ASHG 2016 GATK workshop tutorial on CNV discovery with GATK4. This comprises a test dataset and a precompiled GATK4 executable that was produced specifically for this tutorial. It is not a full release of GATK4 and should not be used for general purposes. To be clear: some of the tools included that are not part of the CNV pipelines are currently in intermediate development stages and may be non-functional.
A worksheet will be made available at the time of the workshop containing detailed instructions on how to run the tutorial.
All POSIX operating systems (Unix, Linux, MacOSX etc) are supported. Microsoft Windows is not supported. The current version requires Java 8. Note that the Oracle Java is preferred; OpenJDK is not officially supported. A few tools require R 3.1.3 (mainly for plotting). An Rscript is included in the bundle (top-level directory) to install any R libraries not already present on your system. This Rscript can be invoked as follows:
The GATK 4 Alpha package is made available for free to academic researchers under a limited license for non-commercial use. Note that GATK 4 is not currently available for commercial use due to its alpha status. The executable provided in the package above may be obtained and used for the purposes of running the included tutorial under the academic license by all users (including employees of commercial companies).