Q:
I seem to remember that you were doing some ENCODE analysis using an actual
NA12878 genome instead of the human reference GRCh37 (or whatever what the
current version at the time). Am I remembering this correctly? Was there
ever a comparison published that showed the benefits of using the actual
NA12878 genome versus the reference?

A:
yes to all above!

this is was in the encode phase 2 manuscript (we did the fig.)
Also, there were detailed follow up analyses in
http://papers.gersteinlab.org/papers/AlleleSeq/
http://papers.gersteinlab.org/papers/alleledb/