How is tumor_f in Funcotator MAF

Answered

Follow

Robert Bremel

• May 26, 2020 17:11

Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.

Using most recent GATK docker.

tumor_f is not one of the columns in the MAF specification.   How is it computed?  

 

 

0

• 

  Bhanu Gandham

  • May 28, 2020 17:23

  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.

   

  0

  Comment actions Permalink
• 

  Wenhong Jiang

  • March 04, 2022 06:04

  I also want to know what's the meaning of ‘tumor_f ’？

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • March 11, 2022 02:48

  Hi Wenhong Jiang, 

  Please see this forum post: https://gatk.broadinstitute.org/hc/en-us/community/posts/360077993111-Tumor-and-Normal-Read-Frequency-vs-tumor-f-value-in-MAF-

  Let me know if you have any further questions.

  Best,

  Genevieve

  0

  Comment actions Permalink

Please sign in to leave a comment.