How can I get AF for each sample in GVC JointGenotyping mode?

Answered

Follow

Jenifer

• November 19, 2020 08:25

Hi!

I have analyzed some samples by running GATK GenotypeGVCF v4.1.7.0. The output VCF contains the following format field `GT:AD:DP:GQ:PL` for each sample. As you can see, there is no AF field for each sample. AF exist in INFO field globally for the variant, with no specification of the specific AF in each sample.

Would it be okay to divide AD / DP for each specific sample, in order to get AF for each one of the samples?

Thanks!

0

• 

  Genevieve Brandt (she/her)

  • November 19, 2020 22:18

  Hi Jenifer,

  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.

  0

  Comment actions Permalink
• 

  woodword

  • December 03, 2020 07:11

  Maybe these two posts could give your some clues

   

  https://gatk.broadinstitute.org/hc/en-us/articles/360047216371-DepthPerAlleleBySample
  https://gatk.broadinstitute.org/hc/en-us/articles/360047217871-Coverage

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • December 04, 2020 17:07

  Thanks for taking the time to help out other users and contribute to the GATK community, woodword!

  0

  Comment actions Permalink

Please sign in to leave a comment.