第二:Coverage Analysis
GetPileupSummaries
ASEReadCounter
CollectAllelicCounts
CollectReadCounts
CountBases
CountBasesSpark
CountReads
CountReadsSpark
GetPileupSummaries
Pileup
PileupSpark
第三:Diagnostics and Quality Control
AccumulateVariantCallingMetrics (Picard)
AnalyzeCovariates
BamIndexStats (Picard)
CalcMetadataSpark
CalculateContamination
CalculateReadGroupChecksum (Picard)
CheckFingerprint (Picard)
CheckPileup
CheckTerminatorBlock (Picard)
ClusterCrosscheckMetrics (Picard)
CollectAlignmentSummaryMetrics (Picard)
CollectBaseDistributionByCycle (Picard)
CollectBaseDistributionByCycleSpark
CollectGcBiasMetrics (Picard)
CollectHiSeqXPfFailMetrics (Picard)
CollectHsMetrics (Picard)
CollectIndependentReplicateMetrics (Picard)
CollectInsertSizeMetrics (Picard)
CollectInsertSizeMetricsSpark
CollectJumpingLibraryMetrics (Picard)
CollectMultipleMetrics (Picard)
CollectMultipleMetricsSpark
CollectOxoGMetrics (Picard)
CollectQualityYieldMetrics (Picard)
CollectQualityYieldMetricsSpark
CollectRawWgsMetrics (Picard)
CollectRnaSeqMetrics (Picard)
CollectRrbsMetrics (Picard)
CollectSequencingArtifactMetrics (Picard)
CollectTargetedPcrMetrics (Picard)
CollectVariantCallingMetrics (Picard)
CollectWgsMetrics (Picard)
CollectWgsMetricsWithNonZeroCoverage (Picard)
CompareBaseQualities
CompareDuplicatesSpark
CompareMetrics (Picard)
CompareSAMs (Picard)
ConvertSequencingArtifactToOxoG (Picard)
CrosscheckFingerprints (Picard)
CrosscheckReadGroupFingerprints (Picard)
EstimateLibraryComplexity (Picard)
EstimateLibraryComplexityGATK
FlagStat
FlagStatSpark
GetSampleName
MeanQualityByCycle (Picard)
MeanQualityByCycleSpark
QualityScoreDistribution (Picard)
QualityScoreDistributionSpark
ValidateSamFile (Picard)
ViewSam (Picard)
第七:Variant Filtering
ApplyVQSR
CNNScoreVariants
CNNVariantTrain
CNNVariantWriteTensors
CreateSomaticPanelOfNormals
FilterAlignmentArtifacts
FilterByOrientationBias
FilterMutectCalls
FilterVariantTranches
FilterVcf (Picard)
VariantFiltration
VariantRecalibrator
第十三:Variant Manipulation
FixVcfHeader (Picard)
GatherVcfs (Picard)
GatherVcfsCloud
LiftoverVcf (Picard)
MakeSitesOnlyVcf (Picard)
MergeVcfs (Picard)
PrintVariantsSpark
RemoveNearbyIndels
RenameSampleInVcf (Picard)
SelectVariants
SortVcf (Picard)
SplitVcfs (Picard)
UpdateVCFSequenceDictionary
UpdateVcfSequenceDictionary (Picard)
VcfFormatConverter (Picard)
VcfToIntervalList (Picard)