Documentation / Structural Variants
Structural Variants and CNVs
Structural-variant analysis is part of Folklore's production Variant Analysis pipeline. It normalizes compatible VCF calls, gathers structural and copy-number evidence, and assigns each supported record to exactly one interpretation framework.
The workflow is caller-neutral: interpretation depends on the normalized event and available evidence, not on the name of the upstream calling tool. Missing fields remain visible as evidence limitations rather than being inferred without support.
Interpretation, Not Variant Calling
Folklore starts from calls already present in the submitted VCF. Read alignment, structural-variant discovery, breakpoint assembly, and upstream caller validation remain the responsibility of the laboratory workflow.
Production Workflow
Read the submitted call
Folklore consumes compatible structural-variant records from the uploaded VCF. It does not call structural variants from sequencing reads.
Normalize the event
Recognized calls are represented consistently as deletion, duplication, inversion, insertion, breakend, or copy-number variant, with genomic span and copy state when supplied.
Annotate clinical context
The pipeline evaluates gene and exon overlap, dosage-sensitive regions, predicted dosage sensitivity, population overlap, and available call-quality evidence.
Assign one framework
Constitutional copy-number loss or gain is assigned to the Riggs 2020 framework. Other eligible nuclear events are handled by the nuclear Variant Analysis framework.
Present an auditable result
The result preserves the owning framework, classification, contributing evidence, genomic content, population context, and limitations for clinical review.
What the Result Can Show
Event summary
Type, chromosome, start and end coordinates, span, copy state, zygosity, and precision when available.
Classification
A five-tier result and the framework that produced it when the record is eligible for automated interpretation.
Genomic impact
Overlapping genes, exons, dosage-sensitive regions, and per-gene dosage evidence.
Population context
Type-compatible overlap against local structural-variant population references.
Call evidence
Available precision, confidence interval, paired-read, split-read, and related quality fields.
Audit trail
Human-readable evidence criteria and a machine-readable breakdown for supported CNV classifications.
Clinical Boundary
Structural-variant classification is clinical decision support. Breakpoint uncertainty, assay coverage, mosaicism, inheritance, phenotype fit, and orthogonal confirmation can materially change interpretation and require qualified review.
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