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

GenomicsDBImport does not recognize option --genomicsdb-update-workspace-path



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    Anton Kovalsky

    Hi Jose Luis Gualdron thanks for your post.

    The --genomicsdb-update-workspace-path option was added well after, which is why you see an error with that version. In the second step, If the GenomicsDB workspace was initially created with such an old version of GenomicsDBImport, it's possible that newer versions of the tool will be unable to do an incremental import into it, as support for incremental import was added fairly recently. Try wiping away anything left by the old GATK version and making sure the steps are all done using the latest version.

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    Jose Luis Gualdron

    Hi Anton,

    thank you so much for reply. Recently, I downloaded the latest version of GATK ( and I'm going to "Redo" all the steps to probe again GenomicsDB.

    If I have any doubt or questions, I won't hesitate to contact you.

    Best regards!

    Jose Luis 

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