Mutect2 somatic mutation calling for plant

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Lina Herliana

• September 15, 2021 01:42

Dear GATK team,

I plan to use Mutect2 to detect somatic mutation variants in my RNAseq data from specific plant tissue. I would like to ask your advice. I collected two genotypes (mutant and normal) from 3 different individuals for each genotype (3 replicates) at four different time points. We prepared mutant and normal samples using the same procedures (same time). I read the explanation of how to use Mutect2 https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2. I assume mutant samples are equivalent to tumor samples in Mutect2. I understand that I cannot use the mode for "tumor with matched normal" as my samples came from different plants (3 replicates), so I will use the tumor-only mode. However, I can use normal samples to generate PoN.

Do you think I can use tumor-only mode with multi-sample features for time-point samples as they are from the same plants? Then I will do the process separately for the replicates (each plant). Could you please advise if my understanding is correct?

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  Pamela Bretscher

  • September 15, 2021 10:41

  HI Lina Herliana,

  I believe you should be able to run Mutect2 in multi-sample mode using your time point samples from the same plant and your PoN. In multi-sample mode, there doesn't need to be a matched-normal for each sample because all normals are pooled together. Here is a link to the Mutect2 FAQ and a previous forum post discussing the applications of Mutect2 multi-sample mode that you may find helpful. Please let me know if this does not answer your question. 

  Kind regards,

  Pamela

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  Lina Herliana

  • September 15, 2021 11:18

  Hi Pamela,

  Yes, it does answer my question.

  Regards,

  Lina

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