Multi sample somatic calling Mutect2

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avrajit

• February 28, 2024 10:45

REQUIRED for all errors and issues:
a) GATK version used:4.5.0
b) Exact command used:
c) Entire program log:

I like to know how  I do variant calling for multiple pairs of  Normal- tumor samples with Mutect2? As I understand multisample option in Mutiect2 is for multiple sample from single patient. 

Then What is the best possible option to combine all the individual VCFs?  

 

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  Gökalp Çelik

  • March 04, 2024 18:45

  Hi avrajit

  We don't have any multi-sample somatic calling workflow for Mutect2 and we don't have a means to combine individual VCFs produced by Mutect2 for routine use due to tags and VCF structure being different than otherwise germline VCF files. However you may use other existing tools out there to combine your files but your mileage may vary. 

  Regards. 

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  avrajit

  • March 05, 2024 11:34

  Hi Gokalp

  Thanks for your response. 

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