If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Java 7/8 Correctness Issues


In your recent announcement email, you mentioned that there are "potential correctness issues" with running current versions of GATK with Java 8. We've run the pipeline both with Java 8 and with Java 7 and didn't observe any issues. Because of Java's binary compatibility, it's not obvious what would cause problems. Could you please expand upon what sort of correctness issues could occur by using Java 8 with the current pipeline?

Thank you,

Best Answer


  • Ben_MBen_M Member

    Hi Geraldine,

    Thank you very much for sharing your experiences and recommendations. It is much appreciated.

    Thanks again,

  • lslisenlslisen Member

    Is there any problem with the BQSR and java 8?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Have a look at Geraldine's answer here. She talks about HaplotypeCaller there, but the answer applies to BQSR as well :smile:


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I just posted more details in the blog here. We didn't see any problems in the BQSR tests.

  • lslisenlslisen Member

    Hi Geraldine,

    Thanks for your explanation.

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