We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Running mutect on RNA-seq samples

gilhgilh Member


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?




  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Gil, sorry for the late response. We haven't validated the use of MuTect on rnaseq data, and I can't say whether it would work or not. You'd definitely need to preprocess according to the GATK rnaseq pipeline recommendations. Beyond that, you're on your own...

Sign In or Register to comment.