Be more explicit about use of VQSR and avoid usage in regional, exome and low coverage cases. It has bad performance characteristics when run on low coverage whole genomes
Improve logic for selecting bwa mem versus bwa align to handle trimming. Use bwa mem when more than half of first 500 reads are longer than threshold of 75. Fixes #50
Add MIT license to top level directory. Thanks to @lbeltrame. #54
STAR support added.
First pass at new approach installer: bootstraps a local python installation using anaconda, then use CloudBioLinux deploy functionality to install data and tools. Allows updatable tools and data from within install application
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen