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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.
Using MuTect for targeted DNA sequencing of miRNAs?
I have patient-normal dataset for targeted sequencing of known miRNAs.
I wanted to know if it is best to use MuTect pipeline to call for variants or independently use GATK on samples and make somatic calls.
The question roots from whether MuTect discards mutations from non-coding sequences at any step of analysis?