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.
Absolutely agree.  Also the run time for this command should not take this long.  The results SHOULD be generated by a build somewhere and this should either parse the metrics to produce a summary or better yet, hit the DB to pull the desired metrics out for reporting (similar to CompareSnpsSummary).