VEP: Add canonical and CCDS annotations for prioritizing transcripts. Ensure dbNSFP annotations added to CSQ tag features
Avoid has_aligned_reads check on VarScan which caused scaling errors (#428). This check already handled as part of VarScan calling. Move test to samtools, where it is needed. This will ened reworking/testing with samtools 0.2.0 calling
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.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Remove development code.
Merge pull request #448 from kern3020/master

enable sacCer2, update urls and fixes some typos
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
pass extra args (for example, --pdb) to the testrunner