- moving snpeff variables into its own grouping. Moved the PERL script associated with snpeff with this grouping
- changed the snpEff config file to point to a database hard is not hardcoded to the genesis scratch space
- modified the varscan recipes to use the new LSCRIPT functions
- moved the VCF_TO_ONELINE PERL script in vcftools to the Makefile.inc
- modified the code in fastq.mk to use the new LSCRIPT method
- changed some of the ordered of the variables in hg19.inc and also added some comments