Convert non-N ambiguous bases to Ns in freebayes output to avoid errors processing with GATK. Fixes #622
Added tool to convert GFF3 files to GTF.
Add gff3->gtf converter to the setup script. Closes #612.

Passing --gff3 to the setup script will perform a GFF3->GTF
conversion on the file before creating the transcriptome files.
Updates to pindel calling to attempt to provide speed ups. Limit current cancer calling evaluation to exome regions with option for refseq genes
Move Chanjo integration to write to SQLite database grouped by batches. Use commandline client instead of API to get loading functionality. #596
Merge bed regions for paired VarDict calling as amplicon awareness is only supported for singleton samples
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