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 works in interactive shell, but not in a script


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    Genevieve Brandt (she/her)

    Hi Guy,

    Thanks for writing into the GATK forum with this issue, I hope we can help you figure out what is going wrong here!

    First, I noticed that you wrote you were using GATK but in the program log it looks like it is running Could you verify that you are running the same GATK version on both the interactive shell and script?

    What order of operations are you running in your script that might be different from the interactive shell? Are you creating the GenomicsDB workspace first and trying to add to it or are you wanting to create a new workspace? 

    It would also be helpful for us to see more of the script you are running, in addition to your command and program log from the shell command.



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