Add RNA-seq example.
Use restructured text formatting for links.
Improve documentation for installation. Add recent bcbio nextgen presentation at Biogen
Enable support for dbNSFP and CADD data integration. dbNSFP integrates through an Ensembl VEP plugin and CADD through GEMINI database creation. #146
Improved flexibility on generating validation plots with mixed recalibration/realignment inputs. Fixes #438
Fix validation plot title generation for non-GATK and minimal inputs. Fixes #438
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
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