Removing benchmark.interval_list from git
--It was causing problems having it in source control
--I would modify it, change branches and then forget that it had changed.
Added runVarScan2.sh script.
--It probably needs some parameter tweaking to produce reasonable results.
updating runStrelka.sh for snps as well as indels
Added option --list_tools to RunBenchmark.
--This prints out the list of available scripts and exits
--Added a LIB_DIR base directory to all of the relative file paths
Fixing documentation typo.
Merge branch 'master' into exome
Catching up to master.
--having benchmark.interval_list in exome but not master was causing issues.

Conflicts:
	RunBenchmark.scala