Is it correct to use Mutect2 to identify somatic variants from cell free DNA or from circulating tumour cells?
Answered
Is it okay to use Mutect2 to identify somatic variants from cell free DNA or from circulating tumour cells?
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Yes!
Please do use Mutect2 for calling variants in cfDNA. And let us know if you run into any difficulties.
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In the Mutect2 Read Orientation Artifacts Workflow, can I use normal FFPE and tumor FFPE samples from the same patients to call somatic variants?
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You can definitely use Mutect2 to call variants on FFPE samples, and in general we recommend using a normal when you can.
I'm not positive I know what you are referring to as the "Mutect2 Read Orientation Artifacts Workflow". Could you post a link here, I could check it out and make sure that it's doing what you need.
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Hi, fleharty,
Thank you for your reply. The link to "Mutect2 Read Orientation Artifacts Workflow" is https://gatk.broadinstitute.org/hc/en-us/articles/360035531132
Please search "A step-by-step guide to the new Mutect2 Read Orientation Artifacts Workflow"
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This is a perfectly sensible step-by-step guide to use. We also provide a Terra workspace that should be more convenient to use.
https://app.terra.bio/#workspaces/help-gatk/Somatic-SNVs-Indels-GATK4
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