So here's the list from GATK v1.3-21-gcb284ee
Available annotations for the VCF INFO field:
ChromosomeCounts
IndelType
HardyWeinberg
SpanningDeletions
NBaseCount
AlleleBalance
MappingQualityZero
LowMQ
BaseCounts
MVLikelihoodRatio
InbreedingCoeff
RMSMappingQuality
TechnologyComposition
HaplotypeScore
SampleList
QualByDepth
FisherStrand
SnpEff
HomopolymerRun
DepthOfCoverage
MappingQualityZeroFraction
GCContent
MappingQualityRankSumTest
ReadPosRankSumTest
BaseQualityRankSumTest
Available annotations for the VCF FORMAT field:
ReadDepthAndAllelicFractionBySample
AlleleBalanceBySample
DepthPerAlleleBySample
MappingQualityZeroBySample
Available classes/groups of annotations:
RodRequiringAnnotation
StandardAnnotation
WorkInProgressAnnotation
ExperimentalAnnotation
RankSumTest
No promises about how accurate this is for any other version.
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