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.
Does this still work?  I've gotten confused about the state of it since CQID started making lane QC builds and they've been associated with AnP.  Maybe @tmooney or @acoffman know?  In other words, does CQID only make lane QC models with the microarray model for sample's `default_genotype_data_id`?