> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/illumina-ffpe-dna-prep-with-exome-2.5/additional-information/microsatellite-instability-msi.md).

# 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](/illumina-ffpe-dna-prep-with-exome-2.5/resource-files.md) for more information - and need to match the reference genome used in the alignment step. 


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