Correctly prepare the GATK version when _JAVA_OPTIONS specified. Fixes #529
Documentation and configuration files for running whole genome structural variant evaluations on NA12878 data
Fusion mode for oncofuse fixed. Implemented disambiguation for STAR fusions
Update documentation on virtualbox installation to avoid pointing to older virtual machines and include new defaults in the latest release. Fixes #530
Update Vagrant VM build to use Ubuntu 14.04 to avoid out of date issues with machine and extensions. Fixes #530
Add plots of structural variant validation sensitivity and precision
Fixes for nglims integration and illumina processing: more cleanly handle error cases
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Merge pull request #531 from mjafin/oncofuse

Fusion mode for oncofuse fixed. Implemented disambiguation for STAR fusi...