# Hierarchy For Package picard.vcf

Package Hierarchies:

- All Packages

## Class Hierarchy

- java.lang.Object
  - picard.vcf.ByIntervalListVariantContextIterator (implements java.util.Iterator<E>)
  - picard.vcf.CallingMetricAccumulator (implements picard.vcf.processor.VariantProcessor.Accumulator<RESULT>)
    - picard.vcf.GvcfMetricAccumulator
  - picard.vcf.CallingMetricAccumulator.Result
  - picard.cmdline.CommandLineProgram
    - picard.vcf.CollectVariantCallingMetrics
    - picard.vcf.FixVcfHeader
    - picard.vcf.GatherVcfs
    - picard.vcf.GenotypeConcordance
    - picard.vcf.LiftoverVcf
    - picard.vcf.MakeSitesOnlyVcf
    - picard.vcf.MergeVcfs
    - picard.vcf.RenameSampleInVcf
    - picard.vcf.SortVcf
    - picard.vcf.SplitVcfs
    - picard.vcf.UpdateVcfSequenceDictionary
    - picard.vcf.VcfFormatConverter
    - picard.vcf.VcfToIntervalList
  - picard.vcf.GenotypeConcordance.Alleles
  - picard.vcf.GenotypeConcordanceCounts
  - picard.vcf.GenotypeConcordanceScheme
    - picard.vcf.GA4GHScheme
    - picard.vcf.GA4GHSchemeWithMissingAsHomRef
  - picard.vcf.GenotypeConcordanceSchemeFactory
  - picard.vcf.GenotypeConcordanceStates
  - picard.vcf.GenotypeConcordanceStates.TruthAndCallStates (implements java.lang.Comparable<T>)
  - htsjdk.samtools.metrics.MetricBase
    - picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
      - picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
    - picard.vcf.GenotypeConcordanceContingencyMetrics
    - picard.vcf.GenotypeConcordanceDetailMetrics
    - picard.vcf.GenotypeConcordanceSummaryMetrics
  - picard.vcf.PairedVariantSubContextIterator (implements java.util.Iterator<E>)
  - picard.vcf.PairedVariantSubContextIterator.VcfTuple

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - picard.vcf.GenotypeConcordanceStateCodes
    - picard.vcf.GenotypeConcordanceStates.CallState
    - picard.vcf.GenotypeConcordanceStates.ContingencyState
    - picard.vcf.GenotypeConcordanceStates.TruthState