Updated script so that it can be run as an array job and thus concatenate R1 and R2 in two different jobs
Altered pipeline. Minor changes to usage.
Altered pipeline. Minor changes to usage.
Minor changes to usage.
Minor changes to usage.
Remove minor error.
New exome target file - VCRome version 2
Major updates to accomodate new annovar and new annotations. Streamlined the generation of the annotation file.