Adding extract.sh simple tool to convert vcf into easy to work with format for R
Adding script which takes 3 vcfs and makes a venn diagram out of them.
running UnifiedGenotyper on each spiked bam to calculate readDepths and alleleFractions for each variant position
Added new AltReadFraction stratification module for varianteval
--It stratifies by alternate allele read fraction
--Edited the SomaticSpike xml files to force it to be included in the build/packaging
Merge branch 'master' into calcAlleleFraction

Merging fix to SomaticSpike invocation.

Conflicts:
	GenerateBenchmark.scala
Added scripts to generate a graph of readFraction distributions
--runeval.sh runs VariantEval on a set of the genotype spikein vcfs
--Adding R script plotAltReadFraction.R to create a graph of readFraction distributions.
--currently both are hard coded and bad
Added dbSnp file to GenerateBenchmark for use in snp calling.
Adding flags to run only FP or only FN analysis in RunBenchmark
Adding runMutect.sh a wrapper to run MuTect

--linked to the benchmark.interval_list to lower mutect runtime
Adding average lines from the plot of AltReadFraction.R
Merge branch 'calcAlleleFraction'
--moving read fraction scripts into master.
--these must be run manually at the moment
Minor script changes
--parameterized makeVenns.R so that it takes accepts a list of files on the command line
--modified makeVennFrom3Plots.sh so that it uses Rscript instead of R.
Merge branch '1v1compare'
--merging in a script to generate a plot from a trio of vcfs
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.