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

germline-resource

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    David Benjamin

    Out hg38 resource is at gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz

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    Juechen Yang

    Thanks. David!

    Jason

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    zyf

    gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz   

    Is this a website ? But when I connect it, I can't enter the webpage and not prompted me  to download the file either. Could you help me?

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    David Benjamin

    This is a google bucket path.  You can download it via gsutil cp (and don't forget to download the index gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz.tbi as well).

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    Juechen Yang

    or try this url in browser:

    https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38/

    you will be able to view files

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    zyf

    Thanks! David and Juechen Yang ! 

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    Brian Wiley

    To Whom can we request that this file af-only-gnomad.hg38.vcf.gz be updated.  It was created 4 years ago.

     

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    Genevieve Brandt (she/her)

    Hi Brian Wiley,

    I apologize for the delayed follow up on your question. I forwarded your request to our developer team. They agreed that it would be useful to get an updated version of the af-only-gnomad.hg38.vcf.gz file but they are not able to assign resources to get it completed at this time.

    If someone else creates this file and wants us to host it, please let us know.

    Best,

    Genevieve

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    Ali Fouad Alhawaj

    Hello Genevieve,

    Do you have any update on whether the af-only-gnomad.hg38.vcf.gz file was or will be updated soon?

    Thanks!

    Ali

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    Genevieve Brandt (she/her)

    Hi Ali,

    Unfortunately we are not able to prioritize the update of this file anytime soon. We are still able to host the file if another user can do the updates.

    Best,

    Genevieve

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