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  • #1

    VCF index creation doesn't finish

    I have encountered the following problem several times. When running GATK RealignerTargetCreator, the program attempts to create the indices for the input VCFs.

    With some of my VCFs, the index creation seems to run actively (CPU usage 100%) for a very long time (5 days before I killed the process) even though normally the tribble index creation takes only <30 minutes. Could this be a bug in the program? Have you come up with a similar problem?

    Yilong
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