Fill in the gaps to cover the most basic needs of a bfx pipeline

[armish]

Following up on @julia326 talk, might worth looking into these tools and see whether we can get them into biokepi:

• Variant annotation
  1. snpEff
  2. or extend varcode to allow VCF annotation
• Structural variant calling
  1. DELLY
  2. LUMPY
• Differential expression
  1. Ballgown