Consider using Cram or Bam adjustments to cut down on filesize

[Gurado]

There is several possibilities to reduce the footprint of bam files that we should consider as an option in the mapping mods.

http://blastedbio.blogspot.com.au/2012/03/bam-verus-cram-07.html

Alternatively / additional the cram tools may be interesting depending on its use with subsequent mods.
http://www.ebi.ac.uk/ena/about/cram_usage