Running mutect on RNA-seq samples
I have RNA-seq data on a "normal" cell line and the same cell line in which a an oncogenic transformation was induced (3 samples of each), and I want to find SNVs that are specific to the transformed lines.
I have followed the GATK best practices for calling variants in RNA-Seq, up to the step of split-N-trim.
I want to use MuTect as the tool for variant calling. However, I'm not sure that its statistical model fits RNA-seq, because the read depth may be highly variable between the "control" and "tumor" samples, because there are large differences in gene expression between the two.
Can I use MuTect for variant calling from RNA-seq data? Which pitfalls should I be aware of?