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RStudio IDE and R libraries ggplot2 and gsalib.

To find out how to do so, you should seek help from your systems administrator. The simplest solution is to install an additional JRE and specify which you want to use at the command-line. If you have a version that does not match the requirements stated above for the version of GATK you are running, the GATK may not run correctly or at all. This should return a message along the lines of ”java version 1.8.0_25” as well as some details on the Runtime Environment (JRE) and Virtual Machine (VM). To test your Java version, run the following command in the shell: java -version All Linux/Unix and MacOS X systems should have a JRE pre-installed, but the version may vary.

Previous versions down to 2.6 required JRE 1.7, and earlier versions required 1.6. Starting with version 3.6, the GATK requires Java Runtime Environment version 1.8 (Java 8). The XCode tools are free but an AppleID may be required to download them. On MacOS X, you may need to install the MacOS Xcode tools. See for relevant information and software downloads. These tools are usually pre-installed on Linux/Unix systems. You will also need to have access to an ANSI compliant C++ compiler and the tools needed for normal compilations (make, shell, the standard library, tar, gunzip). Command-line shell, terminal or console.There are also many good online tutorials you can use to learn the necessary notions.

If you are unfamiliar with any of the following, you should consult a more experienced colleague or your systems administrator if you have one. To follow these instructions, you will need to have a basic understanding of the meaning of the following words and command-line operations. Install all software packages required to follow the GATK Best Practices. For latest documentation and forum click here This information is only valid until Dec 31st 2019. IMPORTANT: This is the legacy GATK Forum Website.