The European Rare Diseases Research Alliance (ERDERA) aims to improve the health and well-being of the 30 million people living with a rare disease in Europe, by making Europe a world leader in Rare Disease (RD) research and innovation, to support concrete health benefits to rare disease patients, through better prevention, diagnosis and treatment. Uppsala University, via National Bioinformatics Infrastructure Sweden (NBIS), is partner of ERDERA with responsibility for a subset of the analyses related to a collaborative Genome re-analysis research pipeline. The objectives for this collaborative effort are: (1) Coordinate a pan-European genomics diagnostic research pipeline beyond the state-of-the-art diagnostic pipeline; (2) Re-analyse existing data moving from a distributed to a federated one to discover new molecular diagnoses from known, and novel, disease-gene associations; (3) Leverage knowledge and develop best practices to improve variant interpretation across disease groups and discover new gene-disease associations; and (4) Facilitate the adoption of knowledge, prepare and share best practice guidelines across disease groups. During this process NBIS will work on specific subtasks. During 2025 and 2026 our focus will be on the detection of mosaic copy number variants, mosaic short variants, novel insertion of repeat elements and annotation of copy number variants. Primary analysis of data in the ERDERA project will be conducted by ERDERA partners at Centro Nacional de Análisis Genómico (CNAG) in Spain, and primary output files will be uploaded to the European Genome Phenome Archive (EGA). NBIS will download the data from EGA and perform secondary analyses locally. We intend to run these analyses on Bianca. After finishing our part of the analyses we will upload the results to EGA. The ERDERA project will run until 2032, but data will be available for us in batches. During 2025 and 2026 we expect to have access to four batches of approximately 5000 whole exome sequence samples. For each batch we have a time window of 4 months to download, analyse, interpret data and upload the results to EGA.