For the complete documentation index, see llms.txt. This page is also available as Markdown.
Microsatellite Instability (MSI)
It is recommend to calculate MSI in 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 for more information - and need to match the reference genome used in the alignment step.
