This documentation is a work in progress and is incomplete.
Please contact developers for more details.
This page describes the default annotation sources included with the service and how to add additional annotation sources.
# General annotation
Source: Ensembl Variant Effect Predictor (VEP) (opens new window) Version: 98.3
# VEP settings used in the annotation service
Updating VEP might break a number of things the ELLA application, and should not be done without thorough testing.
Source: HGNC (opens new window) (ID fetched from either NCBI gene ID, Ensembl gene ID or gene symbol) Version:
Source: RefSeq GFF files (added to VEP)
# Population frequencies
Source: Genome Aggregation Database (gnomAD) (opens new window) Version: 2.0
Updating gnomAD might break a number of things the ELLA application, and should not be done without thorough testing. From v3.0, gnomAD is only available for genome build GRCh38, which is currently incompatible with ELLA anno.
# In-house database
No in-house database is included with the service. To add your own database, you need to ...
# External mutation databases
Source: ClinVar (opens new window)
Updates should be done monthly, timed with ClinVar's releases. To update, run ...
# HGMD (Pro)
Updates should be done quarterly, timed with HGMD's releases. To updated, run ...
# Custom annotation
If you have other data sources you wish to annotate with, you can easily extend the reference data sources by modifying
/ops/datasets.json with your custom data sources. See also the vcfanno documentation (opens new window) for the vcfanno section of
See the (currently non-existent)
/examples repo dir for examples on how to extend ELLA anno with your own data.