| Class | Description |
|---|---|
| CheckFingerprint |
Attempts to check the sample identity of the sequence data in the provided SAM/BAM file
against a set of known genotypes in the supplied genotype file (in either GELI or VCF format).
|
| CrosscheckReadGroupFingerprints |
Program to check that all read groups within the set of BAM files appear to come from the same
individual.
|
| 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.
|
| FingerprintResults |
Class that is used to represent the results of comparing a read group within a SAM file
against one or more set of fingerprint genotypes.
|
| GenotypeReader | Deprecated
Please use VCFFileReader instead of this class.
|
| GenotypeReader.VariantIterator |
Small class to encapsulate an iterator over variants, optionally with a sequence dictionary.
|
| 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.
|
| 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 | Description |
|---|---|
| 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}
|