This version tries to match the latest version used by MSK-Biostats. In particular the new pileup and the latest version of the FACETS package with its support of unmatched normals.
Also uses the method from Biostats to pick the best unmatched normal if a matched normal is not available.
usage::
usage:: FACETS.app/run.sh [--tag TAG] TUMORBAM NORMALBAM