( i tried reading thru prior threads here, but couldn't discern a clear answer to what to do without knowing the probe set up front )

Hi Marshall, thank you for your question - we've not encountered this before but you are more than welcome to give a try and keep us posted! You could create a bed file that spans all the exons (with the known risk that not all exons would necessarily be included and/or "well" covered) and use that for the training procedure. WES is considered "just another panel" on our end and has been done before with our pipeline. You would run in targeted mode, not WGTS. The combination of DNA and RNA data is often a great addition as it adds confidence to certain findings (i.e. fusions, CUPPA prediction, etc) and that can be the input of a single run/analysis - hope this helps 🙂