Germline Resouce

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happyhihello

• July 31, 2020 17:23

Hi

I was using GATK4 to call somatic mutation using tumor only mode. I found that it's hard to find the "af-only-gnomad.vcf.gz" file for parameter:

--germline-resource

because I was using hg19 as the reference and the chromosome style is "chr1,chr2". I just wonder if there is any download link to access the compatible "af-only-gnomad.vcf.gz" for me to use?

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• Official comment

  

  Pamela Bretscher

  • August 20, 2021 13:34

  Hi happyhihello,

  All of the data resources offered by GATK can be found in the Resource Bundle. If the resources you are looking for are not present in the bundle, then they are not supported by the GATK team but other users may be able to provide insight on where to find them.

  Kind regards,

  Pamela

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  happyhihello

  • July 31, 2020 17:25

  I am using GATK4 Mutect2

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  Genevieve Brandt (she/her)

  • August 03, 2020 21:36

  Hi happyhihello,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

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