Cell-free DNA (cfDNA) is double stranded, non-randomly fragmented short (<200bp) DNA molecules circulating in the blood stream as a result of apoptosis, necrosis or active secretion from cells. The amount of cfDNA in blood increases dramatically with cellular injury or necrosis and therefore, can be used as a biomarker as a non-invasive prenatal testing, tumor-derived DNA in plasma, or monitoring the graft health in an organ transplantation. The Genome Transplant Dynamics, a rigorous and highly reproducible universal NGS based method, has been commonly used to utilizes genotype information differences in recipient and donor to quantify donor derived cell-free DNA percent. Here we implement a fully automated Snakemake pipeline on-premise as well as a Cloud implementation to systematize the quantification of donor derived cell-free DNA amount.