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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