Add picard to the RNA-seq alignment step.
Bump Picard max memory to 4g.
Initial framework for supporting effects calculation with Ensembl's variant effect predictor
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Update resource files to support VEP and latest snpEff Ensembl databases. Enable VEP support in Gemini
Add RNA-seq example.
Use restructured text formatting for links.
Improve documentation for installation. Add recent bcbio nextgen presentation at Biogen
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
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
Added explicit sample name into var2vcf_valid.pl
Merge branch 'master' into vardict
Fix validation plot title generation for non-GATK and minimal inputs. Fixes #438
Merge branch 'master' into vardict