I try to change I/O framework rather than internal framework(existing MapReduce and so on). I did try to change other tool in I/O framework, and that was finished successfully. I think GATK also can be changed in I/O framework adding MapReduce. You said to rewrite executive.* and traversals*. Am I just rewrite that frameworks only? I think this project is related gatk.io.*. (Surely, I/O process expend all framework.)
I have been analyze framework, CommandLineGATK -> CommandLineExecutable->GenomeAnalysisEngine->OutputTracker->ArgumentSource || Storage,Stub..