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

Cromwell GATK json list of files



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    Bhanu Gandham

    Hi Kristian Unger


    This is a question for the WDL team. I will have someone from the WDL team get back to you.

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    Kristian Unger

    Super! Thank you! Look forward getting in touch with your collegue!

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    Jason Cerrato

    Hi Kristian Unger,

    I see that you're looking for scripting advice, rather than WDL advice. In this case, I recommend writing a post on with the tag 'Cromwell'. This way you can get advice straight from our Cromwell engineers, who will likely be more helpful.

    It will be helpful to link to the current script you are working and detail what kinds of improvements you are looking for. I hope you find a more elegant solution!

    If you have any questions about GATK or WDL, please don't hesitate to let us know!

    Kind regards,


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