Enable passing options to bwa alignment through resources. Thanks to Severine Catreux for suggestion
Resolve issues with GATK VQSR following joint calling due to MQ distribution from bwa by removing annotations from calculation. Ensure joint called samples have dbSNP annotations
Ensure BED combining and temporary directories happen within safe transactions to avoid race conditions. Thanks to @lpantano
Fix for ncpus with a trailing +.

SLURM info occasionally will send back a number of CPUs as 1+,
this drops the +.
Handle post-population preparation correctly when gemini turned off. Fixes #582
Bump human resource files to use dbNSFP v2.6: chapmanb/cloudbiolinux#181
Remove adjusted parameters for older samtools calls to reset with 1.0 and try to improve performance. Update to latest ipython-cluster-helper
Enable straight merging of separately called variants without joint recalling
Fix bug in creating shared regions for analysis when using a single sample in multiple batches: for instance, when using a single normal sample for multiple tumors. Thanks to Miika Ahdesmaki.
Intergate SMsSH with homebrew build and include new JVM options usage
Add links to UGa talk
doc change wrt rna-seq.
Merge pull request #586 from kern3020/master

doc change wrt rna-seq.
Support Psuedomonas genome build
Decoupled scalpel from mutect and enabled pairing via indelcaller argument
Merge branch 'master' into decouple_mutect
Merge pull request #587 from mjafin/decouple_mutect

Decouple mutect
Generalize indelcaller addition to enable usage from other callers. #587