germline-resource
Answered
Hi
I was using GATK4.1.5 to call somatic mutation using match normal mode. I found that it's hard to find the "af-only-gnomad.vcf.gz" file for parameter:
--germline-resource
because I was using hg38 as the reference and the chromosome style is "chr1,chr2". I just wonder if there is any download link to acceess the compatible "af-only-gnomad.vcf.gz" for me to use?
Thank you!
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Out hg38 resource is at gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz
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Thanks. David!
Jason
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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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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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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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Thanks！ David and Juechen Yang !
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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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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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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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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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