OpenCRAVAT is usable on Amazon Web Services in two ways. The first is an AMI that contains an up to date version of the package and almost all annotators. The second is a CloudFormation workflow which will use the AMI to annotate variants in S3 buckets.
Finding the AMI¶
The AMI is a public community image in the us-east-1 region called OpenCRAVAT-version (for example OpenCRAVAT-1.7.1). Here is a link.
Using the AMI¶
The AMI runs CentOS 7 and consists of two 300 GB volumes, a root/job
volume, and a data volume mounted at
/mnt/ssd. Log in as the default
centos. Modules are located at
/mnt/ssd/oc, and config
files are at
We recommend at least a 4 core, 4 GB machine. Expect to use approximately 300 MB of ram per 1 million variants. OpenCRAVAT will run faster with more cores, as certain parts of the annotation process are parallel. Best performance is achieved by either using an Provisioned IOPS SSD for the modules volume, or choosing an instance with an ephemeral ssd and moving the modules to it.