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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?




  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    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...

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