Comments (1)
gokalpcelik
commented on August 23, 2024
We do not have an equivalent annotation such as DP4 found in samtools and bcftools however if you wish to calculate strandbias from these values we do have strand bias metrics calculated from those supporting reads.
Here is the list of all annotations that HaplotypeCaller can provide
AlleleFraction
AllelePseudoDepth
AS_BaseQualityRankSumTest
AS_FisherStrand
AS_InbreedingCoeff
AS_MappingQualityRankSumTest
AS_QualByDepth
AS_ReadPosRankSumTest
AS_RMSMappingQuality
AS_StrandBiasMutectAnnotation
AS_StrandOddsRatio
AssemblyComplexity
BaseQuality
BaseQualityHistogram
BaseQualityRankSumTest
ChromosomeCounts
ClippingRankSumTest
CountNs
Coverage
CycleSkipStatus
DepthPerAlleleBySample
DepthPerSampleHC
ExcessHet
FeaturizedReadSets
FisherStrand
FragmentDepthPerAlleleBySample
FragmentLength
GcContent
GenotypeSummaries
HaplotypeFilteringAnnotation
HmerIndelLength
HmerIndelNuc
HmerMotifs
InbreedingCoeff
IndelClassify
IndelLength
LikelihoodRankSumTest
MappingQuality
MappingQualityRankSumTest
MappingQualityZero
OrientationBiasReadCounts
OriginalAlignment
PossibleDeNovo
QualByDepth
RawGtCount
ReadPosition
ReadPosRankSumTest
ReferenceBases
RMSMappingQuality
SampleList
StrandBiasBySample
StrandOddsRatio
TandemRepeat
TransmittedSingleton
UniqueAltReadCount
VariantType
You can check their descriptions from the main gatk website.
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