Move selection of single samples from multi-sample VCFs to bcftools instead of GATK. #294
Normalize input BED files with overlapping regions as part of processing pipeline to avoid out of order errors from downstream callers like FreeBayes. Fixes #320
Normalize input BED files with overlapping regions as part of processing pipeline to avoid out of order errors from downstream callers like FreeBayes. Fixes #320
Add AlienTrimmer to program provenance.
Start of replacing RNA-SeQC with some custom plots.

Coverage calculation for 100 random genes to replace the
coverage calculation in RNA-SeQC.

Need to implement exon/intron/coding summaries as well.
Use pysam for calculation of sample coverage, removing dependence on GATK CallableLoci. Work towards chanjo integration for coverage
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen