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
Revert back to GiaB v2.17 VCF and BED reference materials for pipeline examples. Thanks to Severine Catreux
Update freebayes germline calling to be compatible with latest versions: perform quality filter of low quality variants after calling, add vcfallellicprimitives. Update filtering to be more sensitive for heterozygotes
Remove GATK from generate transcript counts.
Provide general utility to handle symlinks: making all symlinks relative and including associated index files. Useful to handle symlinks inside and outside of docker containers
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen