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.
I wonder where I can find the SortGTFFile utility program? The link on the webpage http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_annotation_GeneOverlapAnnotator.html is broken.