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.
Originally I wrote this command to only take models with a single instrument data assigned.  Seeing that CompareSnpsSummary used lane_qc_build, I presume that operations uses this command and the larger, merged-alignment build.  I was attempting to avoid inconsistencies in their usage of the command.