Annotation Cache

VEP Cache

Since the VEP cache is stored on the cloud, an extra layer of organization was added. The cache is organized by VEP cache version / genome build cache version. Running this command with --no-sign-request, will allow you to see the contents of the bucket:

aws s3 ls s3://annotation-cache/vep_cache/
    PRE 102_GRCh38/
    PRE 102_GRCm38/
    PRE 108_GRCh38/
    PRE 108_WBcel235/
    PRE 109_GRCh38/
    PRE 109_WBcel235/
    PRE 110_GRCh37/
    PRE 110_GRCh38/
    PRE 110_WBcel235/
    PRE 111_GRCh37/
    PRE 111_GRCh38/
    PRE 111_WBcel235/
    PRE 113_GRCh37/
    PRE 113_GRCh38/
    PRE 113_WBcel235/
    PRE 114_GRCh37/
    PRE 114_GRCh38/
    PRE 114_WBcel235/
    PRE 115_GRCh37/
    PRE 115_GRCh38/
    PRE 115_WBcel235/

You can then use such a command to sync any genome of interest locally

aws s3 --no-sign-request --region eu-west-1 sync s3://annotation-cache/vep_cache/115_GRCh38/ ./vep_cache/

Or alternatively this command if you are in a cloud setup with multiple genome versions:

aws s3 --no-sign-request --region eu-west-1 sync s3://annotation-cache/vep_cache/115_GRCh38/ ./vep_cache/115_GRCh38/
Footer

This resource was developed by Maxime U. Garcia, bioinformatician at Seqera in Barcelona | Stockholm. It is based on SnpEff and VEP ressources. It was created for the nf-core community, and has been uploaded to S3 with the help of Nextflow and Seqera Platform. All of that was made possible by Open Data on AWS.