Best Practices workflow for RNAseq
This workflow is intended to be run per-sample; joint calling on RNAseq is not supported yet, though that is on our roadmap.
Please see the new document here for full details about how to run this workflow in practice.
In brief, the key modifications made to the DNAseq Best Practices focus on handling splice junctions correctly, which involves specific mapping and pre-processing procedures, as well as some new functionality in the HaplotypeCaller.
Now, before you try to run this on your data, there are a few important caveats that you need to keep in mind.