Install Annotation

Previously Required Steps

• Install
• Run VariantGrid

Download VEP cache

Download your choice of refseq or ensembl vep cache, matching the VEP version in settings.ANNOTATION_VEP_VERSION and the consortium in settings.ANNOTATION[build]["annotation_consortium"].

Extract to settings.ANNOTATION_VEP_CACHE_DIR — by default /data/annotation/VEP/vep_cache (should make a homo_sapiens or homo_sapiens_refseq dir)

Download VEP annotation data

This is the extra data for the plugins

The script below downloads data from the internet if it is public, or variantgrid.com if it is not

${VARIANTGRID_DIR}/annotation/annotation_data/vep_download_37_and_38.sh

See also VEP annotation data manual download

You can verify this with python3 manage.py vep_data_check

Genes / Transcripts

Run the following to get the latest version of cdot transcripts. The command works out the latest cdot data release itself, and skips the work if you already have it (--force to override):

python3 manage.py import_cdot_latest

You can restrict it with --genome-build / --annotation-consortium.

For consistent analyses you also want a GeneAnnotationRelease snapshot matching your VEP version — see Gene and Transcript Version Data.

Annotation install steps

View the "annotation" page, this will be "/annotation" from the server path, eg for a local connection https://localhost:8000/annotation