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gatk4 document index

gatk4 document index

作者: 微笑life | 来源:发表于2018-08-15 10:21 被阅读0次

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)

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