Sort iGenome:  Should you have an exisiting copy of an iGenome, you can change the order by which chromosomes are sorted using this script.  The script goes into WholeGenomeFasta/ and reconstructs the reference genome.fa in a more human like order i.g. 1..19, MT, X and Y (uses sort -V).  It uses the same order for the annotation files.  The script also re-generates the indexes where necesary for consistancy.