Project Summary The NHGRI Centers for Common Disease Genomics (CCDG) program is producing tens of thousands of whole genome (WGS) and whole exome (WES) sequencing datasets as part of multiple disease-focused studies. CCDG projects involve data produced at multiple centers and rely on the use of shared controls. It is therefore imperative to the success of CCDG disease projects that groups work together to produce genome variation maps that include data from different centers and projects. The variant ?callsets? resulting from this effort will be crucial to the broader goals of the NHGRI Genome Sequencing Program (GSP). In this context, the efficient and timely generation of variant calls from aggregated genomic data is a top priority. Working towards this goal has been the primary activity of the GSP Data Analysis Working Group to date. Here, we propose to conduct a collaborative variant calling effort towards the generation of CCDG Freeze2.