# Package picard.fingerprint

package picard.fingerprint

Related Packages
Package
Description
picard
Class
Description
CalculateFingerprintMetrics
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
CappedHaplotypeProbabilities
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.
ConvertHaplotypeDatabaseToVcf
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.
CrosscheckMetric.DataType
The data type.
CrosscheckMetric.FingerprintResult
CrosscheckReadGroupFingerprints
Deprecated.
6/6/2017 Use `CrosscheckFingerprints` instead.
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.
ExtractFingerprint
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
Fingerprint
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
FingerprintMetrics
Class for holding metrics on a single fingerprint.
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.
HaplotypeProbabilities.Genotype
Log10(P(evidence| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}
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.
LiftOverHaplotypeMap
Liftover SNPs in HaplotypeMaps from one reference to another
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.