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Hello, I`m new to GATK and Queue. I understand that we can write a QScript in Queue to generate separate GATK jobs and run them on a cluster of several nodes. Can we implement GATK or Queue on google hadoop?

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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..