Fixed problem with the reference varianble and some shell commands
Fixed problem with the reference varianble with pindel2vcf
Merge pull request #9 from NCI-CCR-GB/master

Added ngCGH rule and fixed some bugs
 Added annotatevcf.rules, novo.rules and made multiple changes on other rules
New rules and new files added here
Merge branch 'master' of https://github.com/zhujack/serpentine