# System internals
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 to create annotated VCFs. You can then use ella-anno-target to prepare additional, ELLA-specific files so that it can be easily imported for interpretation.
# Genes and transcripts
VEP with added RefSeq GFF files, HGNC.
- Uses downloaded HGNC data sources 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
# 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, ...