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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.
Ion Torrent Oncomine Focus Assay Analysis
I am aware that there is no "Best practices" pipeline for Ion Torrent data but I was wondering if there is any way to analyze panel data from the Ion Torrent Oncomine Focus Assay (52 genes and 53 samples). I guess I should use hard filtering but I am not sure how I should process these samples using GATK4.