GATK4 Mutect2 Syntax Error

Hi @tmccarty

This looks like an issue with an older version of the tool wrapper. What happens if you try a different version? FAQ: Changing the tool version

If that is not enough, you are welcome to share the history with one of these jobs. We can help to confirm that at least one of the versions of this tool are installed correctly on that particular server (actually UseGalaxy.org? Or somewhere else) or to report an issue to the administrators. Or, maybe the container this tool is running in needs a correction. We’ll just need an example to get started with.

If this was happening at (your own?) local server instead – is is hard to guess, but you can clarify that and we can help to troubleshoot if you share some details.. Maybe some recent change or update for another part of the server impacted this tool? Possibly how or where the jobs are running?

Let’s start there! :slight_smile: