| Interface | Description |
|---|---|
| Annotation |
An annotation group is a set of annotation that have something in common and should be added at the same time.
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| StandardAnnotation |
This is a marker interface used to indicate which annotations are "Standard".
|
| StandardHCAnnotation |
This is a marker interface used to indicate which annotations are "Standard" for the HaplotypeCaller only.
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| StandardMutectAnnotation |
This is a marker interface used to indicate which annotations are "Standard" for Mutect2 only.
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| Class | Description |
|---|---|
| AlleleFraction |
Variant allele fraction for each sample.
|
| AnnotationUtils | |
| BaseQuality |
Median base quality of bases supporting each allele.
|
| BaseQualityHistogram | |
| BaseQualityRankSumTest |
Rank Sum Test of REF versus ALT base quality scores
|
| ChromosomeCounts |
Counts and frequency of alleles in called genotypes
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| ClippingRankSumTest |
Rank Sum Test for hard-clipped bases on REF versus ALT reads
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| CountNs |
Apply a read-based annotation that reports the number of Ns seen at a given site.
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| Coverage |
Total depth of coverage per sample and over all samples.
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| DepthPerAlleleBySample |
Depth of coverage of each allele per sample
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| DepthPerSampleHC |
Depth of informative coverage for each sample.
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| ExcessHet |
Phred-scaled p-value for exact test of excess heterozygosity.
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| FisherStrand |
Strand bias estimated using Fisher's Exact Test
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| FragmentLength |
Median fragment length of reads supporting each allele.
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| GenotypeAnnotation |
Represents an annotation that is computed for a single genotype.
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| GenotypeSummaries |
Summarize genotype statistics from all samples at the site level
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| HeterozygosityCalculator |
A class containing utility methods used in the calculation of annotations related to cohort heterozygosity, e.g.
|
| InbreedingCoeff |
Likelihood-based test for the consanguinuity among samples
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| InfoFieldAnnotation |
Annotations relevant to the INFO field of the variant file (ie annotations for sites).
|
| LikelihoodRankSumTest |
Rank Sum Test of per-read likelihoods of REF versus ALT reads
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| MappingQuality |
Median mapping quality of reads supporting each alt allele.
|
| MappingQualityRankSumTest |
Rank Sum Test for mapping qualities of REF versus ALT reads
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| MappingQualityZero |
Count of all reads with MAPQ = 0 across all samples
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| OrientationBiasReadCounts |
Count of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate alleles
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| OriginalAlignment |
Original Alignment annotation counts the number of alt reads where the original alignment contig doesn't match the current alignment contig
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| PedigreeAnnotation |
A common interface for handling annotations that require pedigree file information either in the form of explicitly
selected founderIDs or in the form of an imported pedigreeFile.
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| PerAlleleAnnotation |
Apply an annotation based on aggregation data from all reads supporting each allele.
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| PossibleDeNovo |
Existence of a de novo mutation in at least one of the given families
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| QualByDepth |
Variant confidence normalized by unfiltered depth of variant samples
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| RankSumTest |
Abstract root for all RankSum based annotations
|
| ReadPosition |
Median distance of variant starts from ends of reads supporting each alt allele.
|
| ReadPosRankSumTest |
Rank Sum Test for relative positioning of REF versus ALT alleles within reads
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| ReferenceBases |
Local reference context at a variant position.
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| RMSMappingQuality |
Root Mean Square of the mapping quality of reads across all samples.
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| SampleList |
List samples that are non-reference at a given variant site
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| StrandBiasBySample |
Number of forward and reverse reads that support REF and ALT alleles
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| StrandBiasTest |
Class of tests to detect strand bias.
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| StrandOddsRatio |
Strand bias estimated by the Symmetric Odds Ratio test
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| TandemRepeat |
Tandem repeat unit composition and counts per allele
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| UniqueAltReadCount |
Finds a lower bound on the number of unique reads at a locus that support a non-reference allele.
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| VariantAnnotation |
Superclass of all variant annotations.
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| VariantAnnotator |
Annotate variant calls with context information
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| VariantAnnotatorEngine |
The class responsible for computing annotations for variants.
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| VariantAnnotatorEngine.VAExpression |
A container object for storing the objects necessary for carrying over expression annotations.
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| VariantOverlapAnnotator |
Annotate the ID field and attribute overlap FLAGs for a VariantContext against a FeatureContext or a list
of VariantContexts.
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