Revert back to vcfcat with shorter command line and used files in a temporary directory. Handle race conditions with preparing bgzipped BED files for filtering
Change default trimming quality to 5 down from 20.

I think this is the correct way of looking at this debate:

http://genomebio.org/is-trimming-is-beneficial-in-rna-seq/

Dropping down to 5 allows more reads to map in the SEQC
dataset, which is only a good thing.
Add featureCounts as a replacement for htseq-count.

featureCounts is much faster than htseq-count. If
it isn't found, it falls back to use htseq-count.