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.
# Annotation tool: VEP
ELLA anno uses Ensembl's Variant Effect Predictor (VEP) (opens new window) for annotation. Settings are managed in
# Data sources
# Datasets used by anno
|Genome||Human genome GRCh37||GATK Resource Bundle (opens new window)||ELLA currently requires the GRCh37 build of the human genome, and does not support GRCh38.|
|Genes||HGNC||HGNC (opens new window)||Gene ID is fetched from either NCBI gene ID, Ensembl gene ID or gene symbol.|
|Genes||RefGene||UCSC (opens new window)||Used for slicing of gnomAD data.|
|Transcripts||RefSeq (interim)||NCBI||See Golden Helix blog (opens new window).|
|Transcripts||Universal Transcript Archive (UTA)||Biocommons (opens new window)|
|Transcripts||SeqRepo||Biocommons (opens new window)|
|Population frequencies||Genome Aggregation Database (gnomAD)||Broad Institute (opens new window)||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.|
|Population frequencies||In-house database||No in-house database is included with the service, this must be added in your own setup.|
|Mutation database||ClinVar||NCBI (opens new window)|
|Mutation database||Human Gene Mutation Database||Qiagen (Pro version)||Pro version requires a paid subscription, and the dataset is not included in |
# Dataset versions
Current versions of datasets used in the annotation service and scripts/commands for downloading or updating are specified in
# 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.