Improve documentation on germline calling and batching, providing better workflow based documentation (#588). Improve documentation on sample metadata and joint calling (#620)
Merge pull request #626 from mjafin/master

Merge bed regions for paired VarDict calling as amplicon awareness is on...
Fix typos in pipeline documentation
Add more helpful error message when STAR genome is missing.

Closes #615. Thanks to @junchend for the report.
Use the bcbio python, not the one in the user's path.
Improve FreeBayes calling by including options from speedseq and sgasomatic usage, and avoiding high depth filter. Current quality status: http://i.imgur.com/f4PNVFK.png
Increase memory usage

Increase the default memory usage (so that at least the test suite will pass)
Provide template for increasing the processing power of the VM
Merge pull request #629 from pfaucon/patch-1

Increase memory usage
Rework FreeBayes somatic calling filtration to use genotype likelihood based filtering. Uses pythonpy to inject custom bcbio filter into streamed calling process, avoiding need for subsequent transformation of results to add SOMATIC/REJECT flags. Includes latest FreeBayes recommendations on splitting and normalizing MNPs
Add additional FreeBayes filter to remove low frequency calls also present in normals. Provides improvement for FreeBayes false positives
Provide additional sensitivity to FreeBayes filtering to capture more true positives in evaluation
Script to create a more minimal subset of dream synthetic 3 data for testing on AWS runs
Filter out non-chromosomal fusion events.

Closes #625.
Provide exome-only version of DREAM evaluation data for scaled down evaluations
RNA-seq pipeline test default to GRCh37 not hg19.
Use GRCh37 instead of hg19 for the RNA-seq example
Bump pybedtools to latest version to avoid open file handle issues #627
Add extra RNA-seq annotation files to hg19 resources.
Documentation work: Add DREAM synthetic 3 example replacing older cancer sample (#588). Add methylation work to todo list (fixes #618)
Add joint calling documentation and pointer to write up. Fixes #348