GERMQ value calculated in the Mutect2 Force-calling mode

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kai wang

• March 10, 2024 13:22

REQUIRED for all errors and issues:
a) GATK version used:4.2.0.0
b) Exact command used:
c) Entire program log:

I’d like to use the Force-calling mode of the Mutect2 to calculate the GERMQ value similar to that calculated in the Tumor-only mode. Can this be achieved?

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  Gökalp Çelik

  • March 11, 2024 04:21

  Hi kai wang

  Presence of GERMQ annotation requires you to run FilterMutectCalls tool. Can you check if you get this annotation after running FilterMutectCalls?

  Regards. 

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  kai wang

  • March 11, 2024 04:40

  Hi Gökalp Çelik,

  FilterMutectCalls tool successfully solved my problem, thank you for your reply.

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