# System internals

NOTE

This documentation is a work in progress and is incomplete.

Please contact developers for more details.

ELLA anno takes annotation data from several sources (included by default or custom) and uses vcfanno (opens new window) to create annotated VCFs. You can then use ella-anno-target (opens new window) to prepare additional, ELLA-specific files so that it can be easily imported for interpretation.

# Annotation

VEP ...

# Genes and transcripts

VEP with added RefSeq GFF files, HGNC.

Uses downloaded HGNC data sources (opens new window) for fetching HGNC ID from either NCBI gene ID, Ensembl gene ID or gene symbol.
On deposit, RefSeq sources are prioritized per variant as follows: 1. Latest GFF; 2. Interim GFF; 3. VEP default. Lower priority sources are discarded.
Chooses the transcript version that matches the version specified in the genepanel if available, otherwise, chooses latest available version.

# Conversion of manual import data

Conversion of manual import data from ELLA's import module (opens new window) is handled using hgvs (opens new window) and uta (opens new window) modules from biocommons (opens new window).

# Extract PubMed IDs

PubMed IDs for each variant are extracted from ClinVar, as well as HGMD if it has been added.

# Allele check

Each variant REF allele is checked against the genome REF allele. If there is a mismatch, ...

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