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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.
RNA-seq variant calling for somatic
I want to find best practice to do variant calling from this page : https://software.broadinstitute.org/gatk/best-practices/
I have exome-seq and RNA-seq data and I think because the sample is from human cancer, the workflow I need to follow is somatic. I don't see any best practice that use RNA-seq for somatic cell. Any suggestion which best practice I should follow and which data, RNA-seq or exome-seq I should use? Thank you.