Mutect2 doesn't output normal sample name in VCF?

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vctrymao

• January 30, 2020 16:54
• Edited

I am using GATK v3.5, and I am trying to run Mutect2 on a tumor sample with a panel of normals (there is no normal sample). I have run it successfully (gotten VCF output) but I do not see any header for the panel where the normal sample would be. So my header looks like: 

 

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE

 

Is there a way to include this somehow? 

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  Bhanu Gandham

  • January 31, 2020 13:52
  • Edited

  HI vctrymao

   

  We do not support GATKv3 anymore. Please upgrade to GATKv4. Thank you!

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  vctrymao

  • January 31, 2020 18:41
  • Edited

  Hi, I tried this even with GATK4 (4.1.2.0) and still get the same problem

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  Bhanu Gandham

  • February 03, 2020 23:40

  Hi vctrymao

   

  You don't see a normal because you didn't provide one. Panel of normals has a different purpose. Take a look at these docs for more information: https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON-

  https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2

  https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf

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