Best practice to process a multisample mutect2 vcf

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Jenifer

• May 11, 2020 16:59

Hi!

I would like to merge individual vcfs from different patients generated by Mutect2 and then analyze all variants together.

I have been reading mutect2 documentation but there is not much information about this.

What would be the best way to merge those vcf into one? Once merged, is it necessary to perform some processing or the variants are ready to analyze?

Thanks!

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  Bhanu Gandham

  • May 11, 2020 23:48

  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.

   

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  David Benjamin

  • May 14, 2020 01:03

  Jenifer This is a totally reasonable thing to want to do, but it's not within the scope of our pipeline.  The Mutect2 (along with FilterMutectCalls, of course) pipeline generates variant calls from one or more tumor and normal samples from a single individual.  We don't have any tools for comparing variant calls from different individuals, except for a few simple operations in SelectVariants.

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