create a generic make_bed script
create a generic make_bed script

- this script can be run on it's own and work with a variety of queuing
  systems
- a separate script is needed to pass along the files and manage the job
  submission to the queue
- pass along input bam file, a output prefix, and a reference bed file
- option to handle paired and single end reads

dpastling/plethora,dpastling/cnv_pipeline,dpastling/cnv_pipeline,dpastling/plethora,dpastling/plethora