Enable specification of samples in multiple batches: allows a single normal sample to match with multiple tumors. Attach variant calling output to tumor samples and avoid splitting tumor/normal into separate VCFs. Fixes for filtering: avoid ploidy post-filtering and GATK filtering on MuTecT output. #285
Do not require gemini to be on PATH for data updates. Thanks to Nishanth Dandapanthu
Support infrastrcture for passing single tumor-only and tumor with normal panel inputs to cancer variant calling. Provide test case for development. #285 #273
Added support for tumor-only calling and use of normal_panel vcf in mutect.py
Merge pull request #293 from mjafin/master

Added support for tumor-only calling and use of normal_panel vcf in mute...
Avoid reconstitution errors for single tumor-only inputs to variant calling. #293
Add globals option to sample input YAML files. Enables specification of shared files a single time making avoiding copy paste and making updates available. Automatically create globals in template functionality if present
Integrate validation plots into standard workflow. Currently requires manually installation of prettyplotlib into bcbio python site-packages until next release
Fixes global options being looked up by value instead of key.
Remove debugger usage.
Fixes: revert 457cd7641a with better documentation and checking for non-hashable values; sorry @roryk for the issue. Correctly ensure all samples are passed back from validation.
Ensure finding of cutadapt installed in local Anaconda python directory. Fixes #295
Ensure track and browser lines are removed from input BED file before feeding to SnpEff #216
Remove filterInterval passed to snpEff which can cause errors in some cases. Prefer filtering by regions done upstream. #216. Also includes small fix for latest GitHub prettyplotlib visuatlization
Bump to latest ipython-cluster-helper with LSF resource support and shorter tags. #258
Ensure filtering subsets final variant calls to  consistently between GATK and FreeBayes. Fixes #216. Replace GATK filtering with bcftools #294
Ensure prepared BED file gets written to file handle prior to use in filtering since large files need multiple lookups #216
More work on getting bcftools to scale for large file: bgzip and index variant region BED. #216
Fix typo in FreeBayes hard filter
Slightly more sophisticated hard filter for FreeBayes calling that handles low depth and quality filters. #216