Message initial scripts
Clean up some unecessary files
Multiple changes to utilise functions, and standardise inputs. Also testing using HTSlib instead of samtools
Fixed variable name, changed temp file/dir names
Minor change to remove unwanted echo and change temp log name
Major changes include switching to using HTSlib, as suggested on the GATK website, for the reversion to FQ format. Also addition of MarkDuplicates and generation of stats.
Start Stampy script, remove unwanted BWA align script
Fixed alignment commands; added help/usage output; added check for required arguments.
Change of name
Updated to new format using functions
Added usage output and flag to prevent GATK phoning home
Added a function for calling the next step in the pipeline