Initial work towards fixing VarScan's VCF output

This covers most of the use cases, although VarScan also produces
invalid REF records (e.g. CAA/A) which aren't handled yet.

Most of the contribution is by Sean Davis, who graciously agreed to
provide it under a MIT license.

This is needed to handle issue #134.
Include mutect and varscan in default system configuration file
Merge pull request #137 from lbeltrame/fix-varscan-output

Initial work towards fixing VarScan's VCF output
Update main entry point to remove deprecated messaging inputs and generalize to new infrastructure. Prepare for moving into module to allow calling from REST API as well as main launch script.