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
Avoid parallel race conditions when cleaning up after bgzipping. #216
Change quality filter for hets to match distribution of quality scores in current FreeBayes head. Bump ipython-cluster-helper version.
Disambiguation for RNA-STAR fixed: nM tag changed to NM
Merge pull request #302 from mjafin/master

Disambiguation for RNA-STAR fixed: nM tag changed to NM
Avoid issues with numpy 1.7/1.8 discrepency in automated conda installation. Fixes #304
Annotate using the gffutils db if it exists.

Remove mygene method as calling out to external sources can be
problematic in some compute environments.

Resolves #300. Thanks to @mjafin.
Bump to latest ipython-cluster-helper. Fixes #298
Bump to latest ipython-cluster-helper with torque fix
Add --strand-filter 1 to VarScan somatic options

This is done in order to filter variants with extremely high (>90%)
strand bias.
Fix Tophat inner distance calculation.

Read pairs  spanning exons cause outliers in the insert size
distribution. This uses the median and an estimate
of the standard deviation based on the median absolute
deviation which is more stable w.r.t outliers.