# Package picard.fingerprint

- Class Summary
  Class | Description
  --- | ---
  CheckFingerprint | Checks the sample identity of the sequence/genotype data in the provided file (SAM/BAM or VCF) against a set of known genotypes in the supplied genotype file (in VCF format).
  ClusterCrosscheckMetrics | Summary
  ClusteredCrosscheckMetric | A metric class to hold the result of `ClusterCrosscheckMetrics` fingerprints.
  CrosscheckFingerprints | Checks that all data in the set of input files appear to come from the same individual.
  CrosscheckMetric | A class to hold the result of crosschecking fingerprints.
  CrosscheckReadGroupFingerprints | Deprecated. 6/6/2017 Use `CrosscheckFingerprints` instead.
  Fingerprint | Small class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.
  FingerprintChecker | Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.
  FingerprintIdDetails | class to hold the details of a element of fingerprinting PU tag
  FingerprintResults | Class that is used to represent the results of comparing a read group within a SAM file, or a sample within a VCF against one or more set of fingerprint genotypes.
  FingerprintUtils | A set of utilities used in the fingerprinting environment
  FingerprintUtils.VariantContextSet | A class that holds VariantContexts sorted by genomic position
  HaplotypeBlock | Represents information about a group of SNPs that form a haplotype in perfect LD with one another.
  HaplotypeMap | A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.
  HaplotypeProbabilities | Abstract class for storing and calculating various likelihoods and probabilities for haplotype alleles given evidence.
  HaplotypeProbabilitiesFromContaminatorSequence | Represents the probability of the underlying haplotype of the contaminating sample given the data.
  HaplotypeProbabilitiesFromGenotype | Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.
  HaplotypeProbabilitiesFromGenotypeLikelihoods | Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block.
  HaplotypeProbabilitiesFromSequence | Represents the probability of the underlying haplotype given the data.
  HaplotypeProbabilityOfNormalGivenTumor | A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from.
  IdentifyContaminant | Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
  MatchResults | Represents the results of a fingerprint comparison between one dataset and a specific fingerprint file.
  Snp | Class to represent a SNP in context of a haplotype block that is used in fingerprinting.

- Enum Summary
  Enum | Description
  --- | ---
  CrosscheckMetric.DataType |
  CrosscheckMetric.FingerprintResult |
  DiploidGenotype | A genotype produced by one of the concrete implementations of AbstractAlleleCaller.
  DiploidHaplotype | Simple enum to represent the three possible combinations of major/major, major/minor and minor/minor haplotypes for a diploid individual.
  HaplotypeProbabilities.Genotype | Log10(P(evidence| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}