Question Title

* 1. For each tool listed below, please indicate what we should do. If you have never heard of a tool or don't care what happens to it, just don't check anything in that row. 

Keep = keep it in the toolkit as is. Check this option if you have used the tool and it works well enough (with the possibility of improvements to be added on request). 

Rewrite = rewrite this tool from scratch. Check this option if you think the tool's functionality is valuable but the tool itself does not work well enough to be usable in its current form.

Remove = delete it from the toolkit. Check this option if you think the tool's functionality is not useful or if you prefer to use a different tool from another toolkit that has the same functionality but works better for you.


  Keep Rewrite Remove
BeagleOutputToVCF
CallableLoci
CheckPileup
ClipReads
CompareCallableLoci
CountBases
CountIntervals
CountLoci
CountMales
CountReadEvents
CountRODs
CountRODsByRef
CountTerminusEvent
CoveredByNSamplesSites
DepthOfCoverage
DiagnoseTargets
DiffObjects
ErrorRatePerCycle
FastaAlternateReferenceMaker
FastaReferenceMaker
FastaStats
FilterLiftedVariants
FindCoveredIntervals
FlagStat
GCContentByInterval
GenotypeAndValidate
HaplotypeResolver
Pileup
PrintRODs
ProduceBeagleInput
QCRef
QualifyMissingIntervals
RandomlySplitVariants
ReadAdaptorTrimmer
ReadClippingStats
ReadGroupProperties
ReadLengthDistribution
RegenotypeVariants
SelectHeaders
SimulateReadsForVariants
SplitSamFile
ValidateVariants
ValidationSiteSelector
VariantsToBeagleUnphased
VariantValidationAssessor

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