Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

A JAVA Error when running GATKSVPipelineBatch.wdl with GATKSVPipelineBatch.ref_panel_1kg.json


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    Jason Cerrato

    Hi 2tong,

    Happy to see if we can help here. Can you provide a few more details for us so we can better assist you?

    • Are you running this on a personal Cromwell?
    • Which version of GATK are you using?
    • You mentioned you aren't using melt. Are you using cromshell and womtool?
    • Have you disabled melt per the instructions in the documentation?

    Many thanks,


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