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GATK resource bundle alternatives

The GATK resource bundle has been inaccessible for at least a week judging by various comments. It's already been reported on the GATK community forum & github but in the meantime does anyone know if any mirrors exist? I'm specifically looking for the files recommended for human hg38 VQSR

hg38 gatk resource bundle
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updated by GenoMax GenoMax • written by stlba • stlba

I'm also interested in alternatives. My tumor antigen workflow relies on at least two files from their resource bundle and, unfortunately, new users won't be able to run the workflow while the bundle is unavailable. What's even weirder about it is that they've updated the Resource Bundle page (on Jan. 30th) after my question regarding the downtime (on Jan. 29th), but the page still doesn't say anything about the downtime.

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written by spvensko spvensko

1 answer

Looks like the issue is with permissions to list the data in the google bucket. Google periodically tightens security permissions on cloud resources and it results in issues like this until proper permissions are set.

Looking around on the gcp-public-data sources from Broad the following link likely contains files from hg38 resource: https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))

Similar files for hg19/GRCh37 are here: https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg19/v0?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))

There are bwa indexes, dictionaries and VCF files.

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written by GenoMax GenoMax

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