Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?