Picard genotype concordance

A new command is available as of Picard 1.122 to compare two VCF files for the purpose of genotype concordance.

This PR includes the gmt wrapper with tests to run GenotypeConcordance using Picard 1.123.  @iferguson90 is currently working on the packaging of the latest version of PIcard.

This PR also contains a new RefAlign command intended to replace CompareSnpsSummary for new models that use mpileup.  Currently those CompareSnp results are all zeros since it doesn't handle the new file format.  The new command is entirely VCF based.
The next step may be to put everything from here on down into a software result - this command would only resolve the build-specific inputs (looks like @instrument_data and $ref_seq_build).  That way a command could also be added to somatic validation with minimal effort.  This will also allow you to shortcut.  But, it is understandable to do this first to get it running in RefAlign and does not need to all be done in this PR.