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Java 7/8 Correctness Issues

Hello,

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,
Ben

Best Answer

Answers

  • Ben_MBen_M Member

    Hi Geraldine,

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

    Thanks again,
    Ben

  • lslisenlslisen Member

    Is there any problem with the BQSR and java 8?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @lslisen
    Hi,

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

    -Sheila

  • 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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