# References MIP can download many program prerequisites automatically via the mip download application `mip download`. Each pipeline has a yaml file where available references are specified ([rd\_dna](https://github.com/Clinical-Genomics/MIP/blob/develop/templates/mip_download_rd_dna_config_-1.0-.yaml), \[rd*rna]\((*-1.0-.yaml)) and the API is described [here](https://github.com/Clinical-Genomics/MIP/blob/develop/documentation/API/download_references.md). To download the references using MIP, run: ``` $ mip download --reference_dir --config ``` This will submit SLURM jobs that automatically downloads all references specified in the config that is not already present in the reference directory. For a full list of download options, run: ```bash $ mip download --help ``` ## Updating a reference Open the download config corresponding to your pipeline and update or add a new `version_tag` in the reference hash. Update the same version tag together with any metadata changes in the reference\_feature hash, see the API for details. Run the same mip command as above to download your updated reference. To include the changes in the analysis - add your reference to your mip config.yaml file where appropriate. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://clinical-genomics.gitbook.io/project-mip/develop/documentation/references.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.