Instead of using the command line, is it possible to develop a graphical user interface for more efficient use of the tools?
I know there are certain tasks that would perform better using command lines and this is a scientific software but writing commands is a bit troublesome, especially when it is mostly repetitive with only a few tweaks to run similar problems, and I was wondering if there are any better alternatives.
Looking forward to hearing from you.
I have used GATK in my PhD project, and was wondering if I could get the permission to use the Best Practices workflow graphics  in my doctoral dissertation? How should I attribute your copyright?