A Scalable Tool for Democratizing Variant Calling on Human Genomes Using Commodity Clusters

Variant calling is a fundamental task that involves identifying variants in an individual's genome compared to the reference genome. Knowing these variants is critical for assessing an individual's risk for diseases such as cancer and developing new treatments. Due to the large size of human genome sequences, processing and analyzing them requires significant compute and storage resources. Cluster computing is an attractive solution for processing a large workload of human genomes. In this paper, we present a scalable tool for democratizing variant calling on human genome sequences using testbeds that are available for academic research at no charge. Our tool can (a) execute two types of variant calling pipelines in a commodity cluster with CPUs and graphics processing units (GPUs); (b) enable improved cluster utilization and faster execution via asynchronous computations, minimal synchronization, and mutual exclusion when employing GPUs; and (c) execute variant calling pipelines of multiple users concurrently. Using publicly available human genome sequences, users can interactively experience the unique features of our tool, which has a low barrier to entry for large-scale variant calling.