# Microsatellite Instability (MSI) It is recommend to calculate MSI in [tumor-only mode](https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/biomarkers/biomarker-msi#example-command-for-tumor-only-mode). Tumor-only mode relies on a reference directory of files (.dist) containing the microsatellite repeat distribution in a panel of normals. Both the reference directory and microsatellite list are provided - see the [Resource Files page](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/resource-files) for more information - and need to match the reference genome used in the alignment step. --- # 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://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/microsatellite-instability-msi.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.