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.
How to generate RefSeq ROD
I would like to include a RefSeq ROD file in order to get the coverage per gene using the GATK coverage tool (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html). However, it is not really clear to me how I can easily generate such a file, since I can not find the right documentation. All the links that should point to this information seem to be (incorrectly?) redirected to the main GATK homepage). For example this http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html has a link that points to http://www.broadinstitute.org/gsa/wiki/index.php/RefSeq which is redirected to http://www.broadinstitute.org/gatk/.
Can someone point me to the correct docs? Other resources I found also point to the same wiki, which I can't find at the moment..