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Anonymous committed f32a1ee

changes to gatk2.8

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tool-data/gatk2_annotations.txt

 BaseCounts	BaseCounts	BaseCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 BaseQualityRankSumTest	BaseQualityRankSumTest	BaseQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 ChromosomeCounts	ChromosomeCounts	ChromosomeCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-DepthOfCoverage	DepthOfCoverage	DepthOfCoverage	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+ClippingRankSumTest	ClippingRankSumTest	ClippingRankSumTest	VariantAnnotator
+Coverage	Coverage	Coverage	VariantAnnotator
+DepthOfCoverage	DepthOfCoverage	DepthOfCoverage	UnifiedGenotyper,VariantRecalibrator
 DepthPerAlleleBySample	DepthPerAlleleBySample	DepthPerAlleleBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 FisherStrand	FisherStrand	FisherStrand	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 GCContent	GCContent	GCContent	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 HardyWeinberg	HardyWeinberg	HardyWeinberg	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 HomopolymerRun	HomopolymerRun	HomopolymerRun	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 InbreedingCoeff	InbreedingCoeff	InbreedingCoeff	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-IndelType	IndelType	IndelType	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+IndelType	IndelType	IndelType	UnifiedGenotyper,VariantRecalibrator
 LowMQ	LowMQ	LowMQ	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 MVLikelihoodRatio	MVLikelihoodRatio	MVLikelihoodRatio	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 MappingQualityRankSumTest	MappingQualityRankSumTest	MappingQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 SampleList	SampleList	SampleList	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
 SnpEff	SnpEff	SnpEff	VariantAnnotator,VariantRecalibrator
 SpanningDeletions	SpanningDeletions	SpanningDeletions	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-TechnologyComposition	TechnologyComposition	TechnologyComposition	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+StrandBiasBySample	StrandBiasBySample	StrandBiasBySample	VariantAnnotator
+TandemRepeatAnnotator	TandemRepeatAnnotator	TandemRepeatAnnotator	VariantAnnotator
+TransmissionDisequilibriumTest	TransmissionDisequilibriumTest	TransmissionDisequilibriumTest	VariantAnnotator
+TechnologyComposition	TechnologyComposition	TechnologyComposition	UnifiedGenotyper,VariantRecalibrator
+VariantType	VariantType	VariantType	VariantAnnotator