GATK compilation problem

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
This discussion was created from comments split from: Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode..

Comments

  • knhoknho Indiana, USAMember

    Hi Geraldine and pdexheimer,
    Thank you so much for your information.
    We downloaded the GATK source including vectorPairHMM source written by C++. When I built it, it gave me an error message: "Buildfile: build.xml does not exist"

    In addition, after building vectorPairHMM, can I use it in order to call multi-sample variants following the GATK Best Practice steps?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @knho I moved your comment to this new thread because it's not directly related to that other discussion.

    Can you tell us a little more about what you're trying to do exactly, along with command line, full error etc?

    Also, why are you trying to build it yourself instead of just downloading the precompiled package from our Downloads page? The accelerated vectorPairHMM is activated by default in the latest precompiled version.

  • knhoknho Indiana, USAMember

    When we build the GATK source using "ant", we got an error message: "Buildfile: build.xml does not exist"

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    What version are you using? The latest versions use maven instead of ant for building. The build command is mvn verify.

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