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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

Unable to unzip GATK

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    Gökalp Çelik

    Hi Giang Tran

    Looks like your download was not complete therefore you have an invalid archive. 

    Can you use wget or curl to download the file in the following link?

    https://github.com/broadinstitute/gatk/releases/download/4.6.0.0/gatk-4.6.0.0.zip 

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    Giang Tran

    Hey, thank you for the answer! Unfortunately, our current internet connection keeps giving us a hard time downloading through wget. Our current solution is to download gatk from a better internet connection into a portal hard drive and then to transfer it into our Ubuntu machine. The downloads seemed complete but we could not unzip it as mentioned. I would appreciate any advice you can give us given this circumstance.

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    Gökalp Çelik

    Hi Giang Tran

    Here is the md5sum of our zip file. You can check your downloaded file to see if the downloaded or copied file is complete and uncorrupt.

    cbaeef58af8c338d8d7ad44624cfcc03  gatk-4.6.0.0.zip

    I hope this helps.

    Regards. 

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    Giang Tran
    Hi Gökalp Çelik,
     
    Thanks for the answer. Here is what I got from md5sum:
     
    $ md5sum gatk-4.6.0.0.zip
    9eab60f444eecb44e88faebf04700306  gatk-4.6.0.0.zip
     
    Does this mean that the file is corrupted? If so, what would be a good workaround since wget seems to fail every time for me.
     
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    Gökalp Çelik

    Hi again.

    Yes your file seems incorrect and possible corrupt of incomplete. Unfortunately there is no simple workaround for a slow connection. You may need to consult your IT department to provide a solution for your compute environment.

    Regards. 

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