Documentation / Getting Started
Getting Started
Helix Insight receives a VCF file, processes it through a six-stage pipeline, and produces fully classified variants with ACMG evidence, phenotype correlation, literature evidence, and a prioritized shortlist for clinical review.
The Six-Stage Pipeline
VCF Parsing
Your file is read and loaded into the analysis engine.
Quality Filtering
Low-quality variants are flagged. ClinVar pathogenic variants are never discarded.
Annotation
Variant consequences predicted by Ensembl VEP (coding impact, protein effect, splice region).
Reference Database Enrichment
Population frequencies, clinical significance, functional predictions, gene constraint, phenotype associations, and dosage sensitivity loaded from 7 databases.
ACMG Classification
19 automated criteria evaluated, Bayesian point-based classification applied, confidence scores assigned.
Export
Results ready for clinical review. Gene-level summaries available immediately.
Processing Time
Gene panels complete in under 2 minutes, whole exome sequencing (WES) in 2-5 minutes, and whole genome sequencing (WGS) in 7-15 minutes on dedicated hardware.
What the Platform Does Not Do
Helix Insight does not diagnose. It does not replace the geneticist. It automates the evidence-gathering step of variant interpretation. The geneticist reviews the evidence, applies clinical judgment, considers family history and clinical context, and makes the final clinical decision.
Maximum Sensitivity Approach
No frequency-based or impact-based pre-filtering is applied at any stage. A common variant with a gnomAD allele frequency of 40% still receives a classification -- it will be classified as Benign via BA1, but it is not silently discarded before classification. Nothing is hidden from the reviewing geneticist. The clinician decides clinical relevance based on the complete classification and annotation data.
In This Section
Uploading a VCF File
Supported formats, genome build requirements, and what happens after upload.
Setting HPO Terms
How to provide patient phenotype information and why it matters for prioritization.
Understanding Results
How to read the results interface -- classifications, scores, and annotations explained.
Quality Presets
Three quality filtering levels and the ClinVar rescue mechanism.