vcf files for BQSR step

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Varun Gupta

• March 30, 2020 22:13

Hi,

I am using gatk4 BaseRecalibrator command and I need a known vcf file to input for --known-sites argument. Where can I download the vcf file?

GATK is installed on our cluster and I have read that I can download it from resource bundle, but I cannot find it.

Hope to hear from you guys soon.

 

Regards

Varun

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  Bhanu Gandham

  • April 01, 2020 19:45

  Hi ,

  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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  manolis

  • April 17, 2020 06:57

  Hi,

  take a look in this gatk bucket and here the files to download and the related pipeline

  Best

   

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  Khalil Jahed

  • October 26, 2020 22:09

  Similar question I have. How can one find these known sites for non-model organisms eg. crops? 

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  Genevieve Brandt (she/her)

  • November 02, 2020 16:32
  • Edited

  Khalil Jahed information about the data we provide is here: Resource Bundle

  Other GATK users may be able to provide information about how they found resources for non-model organisms. 

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