API reference¶
Start with Getting started for examples, or choose a topic
below for signatures, parameters, and return types. Most annotation uses the
same effects() interface; annotator selection
is optional.
Read API conventions for return shapes, missing results, error defaults, compatibility names, and current typing coverage.
| Task | Reference |
|---|---|
| Resolve chromosome names for another reader | Chromosome resolver |
| Annotate additional reference ORFs or mapped RNA products | ORFs |
| Compare sample evidence | Sample identity |
Variants and files¶
- Genome
- Variant
- VariantCollection
- StructuralVariant
- parse_symbolic_alt
- SV_TYPES
- Genotype
- Zygosity
- transforms.pair_breakends
- transforms.left_align_indels
- load_vcf
- load_maf
- load_maf_dataframe
- ReferenceMismatchError
- SampleNotFoundError
- GenomeBuildMismatchError
- HypothesisLimitError
Effects¶
- MutationEffect
- NonsilentCodingMutation
- MultiOutcomeEffect
- EffectCollection
- EffectCandidate
- effect_priority
- top_priority_effect
Phasing and germline¶
Phasing and germline reference
- ReadPhasingSource
- MutantTranscriptSource
- MolecularPhaseResolver
- ReadPhaseResolver
- RNAReadPhasingSource
- VCFPhaseResolver
- query_in_cis
- apply_phase_resolver_to_effects
- GermlineContext
- Completeness
- predict_germline_aware_effect
- apply_germline_to_transcript
- partition_germline_by_phase
- PhasePartition
- enumerate_phase_hypotheses
- detect_germline_overlap
- GermlineAlleleOverlap
- detect_loh
- default_germline_window
RNA and transcripts¶
- load_exacto_fusions
- make_fusion_outcome
- RNAEvidence
- MutantTranscript
- apply_variant_to_transcript
- apply_variants_to_transcript
- RNAEvidenceResolver
- NullRNAEvidenceResolver
- apply_rna_evidence_to_effects
- make_rna_outcome