Improved documentation on adding pre-existing genomes to bcbio. #440
Improve snpEff version detection during installation to use manifest version if available. Thanks to Glen Otero
Allow . to be a pair-file separator.
Ensure validate plots passed to upload directory. #438
Skip the sailfish unit test.
Added REJECT flag for non-SOMATIC paired FreeBayes calls
Added REJECT FILTER-field into paired FreeBayes calling
Update configuration.rst for ...

Description of paired variant calling
Scaling improvements: avoid using uncompressed BAMs in pipelines which breaks sambamba on large files (#445). Provide better checks for zlib compressed ipython messages to avoid errors on truncated results
Merge pull request #443 from mjafin/master

FreeBayes: Reject non-somatic mutations in FILTER field
Merge pull request #444 from mjafin/patch-4

Update configuration.rst for ...
Merge branch 'master' into vardict
VarDict -F flag added
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