vcf file for mm39 somewhere?

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Sarah Bonnin

• June 23, 2021 10:12

Hello,

Where do I find a vcf file of known variants for the mm39 assembly? Is it available somewhere?

I want to run the "RNAseq short variant discovery" pipeline on RNA-seq data that were already analysed (differentially expression analysis) using that assembly, so I would like to continue with it, if possible.

Thank you

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  Pamela Bretscher

  • June 23, 2021 13:01

  Hi Sarah,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the non-human topic is for reporting bugs and issues with GATK.
  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  
  Best,
  Pamela

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  Sarah Bonnin

  • June 28, 2021 12:11

  Hi Pamela,

  Please, do so, thank you!

  And sorry for posting to the wrong forum.

  Best

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  Genevieve Brandt (she/her)

  • July 13, 2021 23:32

  Hi Sarah Bonnin,

  Thanks for writing into the forum! Unfortunately I don't think that we have that resource available in our resource bundle. Here are the details about our resource bundle: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle

  We just released an article going over the known sites resources that are used for VQSR, and even though you are not running VQSR, these descriptions might be helpful to get the resource you need: https://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-

  Sorry we don't have the solution!

  Best,

  Genevieve

   

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