Added dbSnp file to GenerateBenchmark for use in snp calling.
Adding runMutect.sh a wrapper to run MuTect
Adding flags to run only FP or only FN analysis in RunBenchmark
Added an interval file to runMutect to make it only run in the relevant interval.
Inverting flags from fp to nofp because gatk arguments didn't work the way I thought.
Fixing issue in runMutect.sh
Yet another fix to runMutect