Support samtools-driven joint calling. Fix checks for using bcbio-variation-recall to ensure resources used in calculating requirements
Avoid race conditions when preparing tabix indexed files during initial BED prep steps. Thanks to @mjafin
Bring unit tests up to date with latest changes to trimming and transactions. Fixes #590. Fixes #591
v0.8.2 release
Provide improved sensitivity for Platypus calling by removing allele bias, qual by depth and mapping quality filters. These remove a number of true positives in NA12878 evaluations
Avoid race conditions during bedprep work on samples with shared input BED files. Fixes #595
Update testing.rst

Updated the RNASeq example for a typo
Merge pull request #599 from pfaucon/patch-1

Update testing.rst
Ensure directory outputs exist when moving from global transaction directories. Thanks to @mjafin and @roryk. Adjust Platypus parameters to match best sensitivity/specificity with NA12878 comparions
Move supported genomes and indexes to be importable.
Update setting up a custom genome from user-provided sequences.

This picks up the installation location of tools and genomes
from the bcbio_system.yaml file. It also removes the dependency of
having cloudbiolinux installed.
add pindel
pindel integration as indels caller together with mutect
remove import and correct is_installed function
Skip fixing the PI read group if it does not exist.
Remove merging of bed files in _subset_bed_by_region

Handle merging within variant callers if necessary (e.g. FreeBayes)
Added an option into bed prep to not merge overlapping regions. Useful for VarDict amplicon aware calling.
Update run_tests.sh

Handle paths with spaces.

The absolute path to bcbio_nextgen.py may have spaces, symlinks notwithstanding. In this case, dirname tokenizes the output of readlink as multiple strings, and this propogates to the last line of the script. Quoting suffices.
Merge pull request #611 from etal/patch-1

Handle paths with spaces in run_tests.sh
Remove mosaik reference from documentation. Thanks to @inti. Fixes #608