Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

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?

nroaknroak HoustonMember ✭✭

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?

Best Answer

Answers

  • nroaknroak HoustonMember ✭✭

    Thanks Kristian for the reply. Is there a way to get around by using data for miRNAs that are covered by exome capture? To my understanding, most exome captures cover ~700-800 miRNAs in the chip.

Sign In or Register to comment.