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How to switch to a different Java version when running GATK?

adam_diadam_di PKUMember
Dear GATK developers,
My system's default java version is 11.0.1, but I know java 1.8 is recommended running GATK. I also have java 1.8 installed on the system. And GATK is recommended to be executed using command 'gatk' instead of 'java -jar gatk-*.jar'. How can I tell gatk to use a different version of Java? Thank you.

Best Answer


  • bshifawbshifaw admin Member, Broadie, Moderator admin

    I'll have to double check if parameters exist within the gatk wrapper script to allow you to specify the java version. But if your in a rush you could temporarily change the default java being used on you system as mentioned on this site.

  • bshifawbshifaw admin Member, Broadie, Moderator admin

    Hi Adam,

    There isn't a quick way to specify the Java version when running GATK with the wrapper script, the java version would have to be temporarily set as the default on your system as mentioned above.

  • adam_diadam_di PKUMember
    Thank you all! It has been solved.
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