gnomAD version in Mutect2 bundle

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Guruprasad Ananda

• March 03, 2020 20:28

Hi, which version of gnomAD (2.x.x) and which cohort (exomes or genomes) was used to build the gnomAD VCF file (af-only-gnomad.raw.sites.b37.vcf) that you provide with your mutect2 resource bundle? Thanks.

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  Bhanu Gandham

  • March 04, 2020 00:03

  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.

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  Pieter Lukasse

  • March 04, 2020 21:54
  • Edited

  Hi Bhanu Gandham,

  I don't think it is fair to push this to the community given that probably only the GATK team can really know the answer to this question... unless the scripts to generate the bundle at https://gatk.broadinstitute.org/hc/en-us/articles/360036212652-Resource-Bundle are made available somewhere...  If you can at least link us to the team that maintains these bundles, that will be highly appreciated.

  Thanks,

  Pieter

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  David Benjamin

  • March 05, 2020 18:01

  Pieter Lukasse Fair point.  The script to generate the AF-only gnomAD is public and available in the gatk repo: https://github.com/broadinstitute/gatk/blob/master/scripts/mutect2_wdl/mutect_resources.wdl.

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  Pieter Lukasse

  • March 06, 2020 16:52

  Thanks David Benjamin! I will check it out. 

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