# Package picard.vcf

- Class Summary
  Class | Description
  --- | ---
  AccumulateVariantCallingMetrics | Combines multiple Variant Calling Metrics files into a single file.
  ByIntervalListVariantContextIterator | Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
  CallingMetricAccumulator | Collects variants and generates metrics about them.
  CallingMetricAccumulator.Result |
  CollectVariantCallingMetrics | Collects summary and per-sample metrics about variant calls in a VCF file.
  CollectVariantCallingMetrics.VariantCallingDetailMetrics | A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
  CollectVariantCallingMetrics.VariantCallingSummaryMetrics | A collection of metrics relating to snps and indels within a variant-calling file (VCF).
  FixVcfHeader | Tool for replacing or fixing up a VCF header.
  GA4GHScheme | The scheme is defined in the constructor.
  GA4GHSchemeWithMissingAsHomRef | The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
  GatherVcfs | Simple little class that combines multiple VCFs that have exactly the same set of samples and totally discrete sets of loci.
  GenotypeConcordance | Summary
  GenotypeConcordance.Alleles | A simple structure to return the results of getAlleles.
  GenotypeConcordanceContingencyMetrics | Class that holds metrics about the Genotype Concordance contingency tables.
  GenotypeConcordanceCounts | A class to store the counts for various truth and call state classifications relative to a reference.
  GenotypeConcordanceDetailMetrics | Class that holds detail metrics about Genotype Concordance
  GenotypeConcordanceScheme | This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
  GenotypeConcordanceSchemeFactory | Created by kbergin on 6/19/15.
  GenotypeConcordanceStates | A class to store the various classifications for: 1.
  GenotypeConcordanceStates.TruthAndCallStates | A minute class to store the truth and call state respectively.
  GenotypeConcordanceSummaryMetrics | Class that holds summary metrics about Genotype Concordance
  GvcfMetricAccumulator | An accumulator for collecting metrics about a single-sample GVCF.
  LiftoverVcf | Summary
  MakeSitesOnlyVcf | Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
  MakeVcfSampleNameMap | Creates a TSV from sample name to VCF/GVCF path, with one line per input.
  MergeVcfs | Combines multiple variant files into a single variant file.
  PairedVariantSubContextIterator | An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
  PairedVariantSubContextIterator.VcfTuple | Little class to hold a pair of VariantContexts that are in sync with one another.
  RenameSampleInVcf | Renames a sample within a VCF or BCF.
  SortVcf | Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.
  SplitVcfs | Splits the input VCF file into two, one for indels and one for SNPs.
  UpdateVcfSequenceDictionary | Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
  VcfFormatConverter | Converts an ASCII VCF file to a binary BCF or vice versa.
  VcfToIntervalList | Converts a VCF or BCF file to a Picard Interval List.
  VcfUtils | Created by farjoun on 4/1/17.

- Enum Summary
  Enum | Description
  --- | ---
  GenotypeConcordanceStateCodes | Created by kbergin on 7/30/15.
  GenotypeConcordanceStates.CallState | These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.
  GenotypeConcordanceStates.ContingencyState | A specific state for a 2x2 contingency table.
  GenotypeConcordanceStates.TruthState | These states represent the relationship between a truth genotype and the reference sequence.