To address the computational limitations and optimize the cost, we have developed
COSMOS (http://cosmos.hms.harvard.edu) , a scalable, parallelizable workflow management system running on clouds (e.g.,
Amazon Web Services or Google Clouds). Using COSMOS 1], we have constructed a NGS analysis pipeline implementing the Genome Analysis Toolkit
– GATK v3.1 – best practice protocol 2,3], a widely accepted industry standard developed by the Broad Institute. COSMOS performs
a thorough sequence analysis, including quality control, alignment, variant calling
and an unprecedented level of annotation using a custom extension of ANNOVAR. COSMOS
takes advantage of parallelization and the resources of a high-performance compute
cluster, either local or in the cloud, to process datasets of up to the petabyte scale,
which is becoming standard in NGS.