Question: What is the different if I call germline SNP/Indel with mutect and HaplotypeCaller?
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gravatar for Makplus T
15 months ago by
Makplus T70
Makplus T70 wrote:

Hello,

I have noted that, as designed for somatic variants caller, MuTect2 includes some logic to skip variant sites that are very clearly germline based on the evidence present in the Normal sample compared to the Tumor sample, for avoiding spending computational resources on germline events.

And it is NOT capable of emitting records for variant calls that are clearly germline unless it is run in artifact-detection mode, which is used for Panel-Of-Normals(PoN) creation.

So, here is my question:

  1. Could I call germline variants just using Mutect with single tumor mode? (just like the way we create the PoN)
  2. Could I use the PoN as the germline variants?

Have a good day!

haplotypecaller. mutect gatk • 507 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by Makplus T70
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