CalculateFingerprintMetrics |
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
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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).
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ClusterCrosscheckMetrics |
Summary
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ClusteredCrosscheckMetric |
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CrosscheckFingerprints |
Checks that all data in the set of input files appear to come from the same
individual.
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CrosscheckMetric |
A class to hold the result of crosschecking fingerprints.
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CrosscheckReadGroupFingerprints |
Deprecated.
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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.
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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.
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FingerprintIdDetails |
class to hold the details of a element of fingerprinting PU tag
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FingerprintMetrics |
Class for holding metrics on a single fingerprint.
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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.
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FingerprintUtils |
A set of utilities used in the fingerprinting environment
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FingerprintUtils.VariantContextSet |
A class that holds VariantContexts sorted by genomic position
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HaplotypeBlock |
Represents information about a group of SNPs that form a haplotype in perfect LD
with one another.
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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.
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HaplotypeProbabilities |
Abstract class for storing and calculating various likelihoods and probabilities
for haplotype alleles given evidence.
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HaplotypeProbabilitiesFromContaminatorSequence |
Represents the probability of the underlying haplotype of the contaminating sample given the data.
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HaplotypeProbabilitiesFromGenotype |
Represents a set of HaplotypeProbabilities that were derived from a single SNP
genotype at a point in time.
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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.
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HaplotypeProbabilitiesFromSequence |
Represents the probability of the underlying haplotype given the data.
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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.
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IdentifyContaminant |
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and
uniform in the genome.
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MatchResults |
Represents the results of a fingerprint comparison between one dataset and a specific
fingerprint file.
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Snp |
Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
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