Yeah, I don't see why it wouldn't be.  You run BQSR over a single ADAM directory (we need a different name for this, maybe "ADAM RDD" or "ADAM set"?) -- and you get particular model and a particular re-calibrations of the QSes.  

Now, if you arbitrarily split the BAM N ways, and then recombined them *before* running BQSR, I don't see why that should affect the recalibration.  

I don't have any reason to think that your solution here doesn't work, I just was wondering out loud.  It seems like one of these kinds of requirements that Carl and I have been coming to grips with, and I wasn't sure if it had already been part of everyone else's thinking or if it deserved a space to be made more explicit.