It looks like you're new here. If you want to get involved, click one of these buttons!
If I put my input files as a list in the file named "input.list", how do I set the output names? or do I just need to set the output folder and the output file names will be automatically named?
Depends which tool you are running, but generally speaking you define the main output file name with -o. Be sure to look at the Technical Documentation pages for the tools you want to use; they contain full details about all the different arguments and controls.
Geraldine Van der Auwera, PhD
thanks for your reply, Geraldine. I am using GATK - HaplotypeCaller. If I feed it with a list of input files, do I just need to provide the "-o" with a output folder, something like this "-o /path/to/Var_out/" ?