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gatk4.beta.2 :IndexFeatureFile problem

luoshizhiluoshizhi Member
edited August 2017 in Ask the GATK team

I am trying to ues IndexFeatureFile to reindex a vcf
gatk-launch IndexFeatureFile -F redo.vcf
however,that command exits with this message:

A USER ERROR has occurred: The IndexFeatureFile tool is temporarily disabled.

org.broadinstitute.hellbender.exceptions.UserException: The IndexFeatureFile tool is temporarily disabled.
    at org.broadinstitute.hellbender.tools.IndexFeatureFile.doWork(IndexFeatureFile.java:60)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:116)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:173)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:131)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:152)

It is a bug?

Best Answer


  • @Geraldine_VdAuwera said:
    As noted in the error message, the IndexFeatureFile tool was temporarily disabled. This was indeed done because of a serious bug in htsjdk. It's being fixed and we should be able to reactivate this tool in a release coming very soon (possibly end of the week).

    thanks,I have used bgzip and tabix solve my problem.

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