Next Generation Sequencing (NGS) is becoming increasingly used in clinical settings for the genomic analysis of germline and cancer samples. Hence, there is a need to establish guidelines that cover the minimum quality requirements for the generation of whole genome sequencing (WGS) and whole exome sequencing (WES) data. NGS pipelines are comprised of several elements, all of which contribute to the end quality of the result, from the reception of the samples to delivery of the outcomes. For this reason, quality control (QC) steps should be incorporated into the workflow to ensure that the data is fit for use, and its usage poses no risk to the patient.