Label structural variant output files by batches, allowing multiple batches to be run on the same input BAM files for partially overlapping analyses. Fixes #513
Use mm10 in the documentation instead of GRCm38.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Update paired variant calling information
Vardict added to the list of somatic ..

variant callers
Merge pull request #524 from mjafin/patch-1

Update paired variant calling information
Merge pull request #525 from mjafin/patch-2

Vardict added to the list of somatic ..
Remove some cruft from the cufflinks test.
Improved structural variant validation: split validated results from event size to identify strengths of individual callers
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Update Vagrant VM build to use Ubuntu 14.04 to avoid out of date issues with machine and extensions.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...
Disambiguate and fusion fields updated in docs

Hi Brad,
I've included some documentation on fusion detection and disambiguation.
Whenever you think this is good to be included, please merge
Initial work evaluating SMaSH. Not finished or integrated into bcbio processing