The ATAV database is a relational database that stored a universal variant list across all samples, variant annotation data, sample variants calls and associated quality metrics, as well as all site’s coverage data for inferring reference alleles at non-call sites. It uses Percona Server for MySQL and its high-performance storage engine Percona TokuDB to improve scalability and operational efficiency.
Our experience with this platform on a database carrying more than 100,000 samples indicates that a relational database can be optimized in a way that makes it possible to analyze current large-scale genomic datasets.
Check docker to setup in docker for test/dev purpose.
Check ec2 to setup in AWS EC2 for production purpose.
Check db_load to setup demo scripts for parsing VCF, BAM and load data into ATAV database.