Install Annotation - SACGF/variantgrid GitHub Wiki

Previously Required Steps

• Install
• Run VariantGrid

Download VEP cache

Download your choice of refseq or ensembl vep cache

Extract to /data/annotation/VEP/vep_cache (should make a Homo_Sapiens 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

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

Annotation install steps

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