Alignment |
Alignment.
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Alignment.Builder |
RecordBuilder for Alignment instances.
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Dbxref |
Database cross reference in GFF3 style DBTAG:ID format.
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Dbxref.Builder |
RecordBuilder for Dbxref instances.
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Feature |
Feature, such as those represented in native file formats BED, GFF2/GTF,
GFF3, IntervalList, and NarrowPeak.
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Feature.Builder |
RecordBuilder for Feature instances.
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Fragment |
The DNA fragment that was targeted by the sequencer, resulting in
one or more reads.
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Fragment.Builder |
RecordBuilder for Fragment instances.
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Genotype |
Genotype.
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Genotype.Builder |
RecordBuilder for Genotype instances.
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OntologyTerm |
Ontology term cross reference in GFF3 style DBTAG:ID format.
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OntologyTerm.Builder |
RecordBuilder for OntologyTerm instances.
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ProcessingStep |
Description of a computational processing step.
|
ProcessingStep.Builder |
RecordBuilder for ProcessingStep instances.
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Read |
Sequence with quality scores.
|
Read.Builder |
RecordBuilder for Read instances.
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ReadGroup |
Read group.
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ReadGroup.Builder |
RecordBuilder for ReadGroup instances.
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Reference |
A reference is a canonical assembled contig, intended to act as a
reference coordinate space for other genomic annotations.
|
Reference.Builder |
RecordBuilder for Reference instances.
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Sample |
Sample.
|
Sample.Builder |
RecordBuilder for Sample instances.
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Sequence |
Contiguous sequence from an alphabet, e.g.
|
Sequence.Builder |
RecordBuilder for Sequence instances.
|
Slice |
View of a contiguous region of a sequence.
|
Slice.Builder |
RecordBuilder for Slice instances.
|
TranscriptEffect |
Annotation of a variant in the context of a feature, typically a transcript.
|
TranscriptEffect.Builder |
RecordBuilder for TranscriptEffect instances.
|
Variant |
Variant.
|
Variant.Builder |
RecordBuilder for Variant instances.
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VariantAnnotation |
Variant annotation.
|
VariantAnnotation.Builder |
RecordBuilder for VariantAnnotation instances.
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VariantCallingAnnotations |
This record represents all stats that, inside a VCF, are stored outside of the
sample but are computed based on the samples.
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VariantCallingAnnotations.Builder |
RecordBuilder for VariantCallingAnnotations instances.
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