Initial work for supporting joint calling/squaring off. Provide framework and initial parallelization points for workflow
Joint squaring off: implement grouping and regional splitting for distributed parallelization
updated URL
the config file for the system is called bcbio_system.yaml
updated URL for freebayes
add yeast genome
Update bcbio conda build to support latest bcbio-nextgen-vm. Clean up Dockerfile
upgrade to a more recent genome for sacCer 2 => 3
Bug fix for correctly grouping multi-caller/multi-batch variant calls
Joint squaring off: add initial integration with bcbio-nextgen-recall, needs additional work to handle regional calling
Easier prep for custom genomes.

This hooks until the cloudbiolinux preparation stuff and is
super hacky but as a place to get started making this a little bit
easier.
Remove development code.
Joint/batch calling: Merge regional batches into single final batch. Correctly reconstitute orignal variation files if calling and joint calling both done. Feed joint callers into gemini database creation instead of initial calls
Fix joint calling test data to use correct ploidy and have additional reference call tests
Integrate LOFTEE VEP plugin from @konradjk to support annotating predicted loss of function variations