Microsatellite Instability (MSI)

MSI is under active development.

If MSI values are needed ahead of software updates, it is recommend to calculate MSI on the tumor files in tumor-only mode in a separate DRAGEN analysis. Tumor-only mode relies on a reference directory of files (.dist) containing the microsatellite repeat distribution in a panel of normals. Also, it is recommended use a custom WES microsatellite list provided. Both the reference directory and microsatellite list are provided in a BSSH project/ICA bundle - see the Resource Files page for more information - and need to match the reference genome used to create the collapsed BAM in the preprocessing step.

/opt/dragen/$VERSION/bin/dragen
--msi-command tumor-only
--max-base-quality 63
--msi-microsatellites-file ${microsatellite_file}  
--msi-ref-normal-dir ${normal_reference_directory} 
--ref-dir $REF_DIR                     
--output-directory $OUTPUT   
--output-file-prefix $PREFIX 
--tumor-bam-input $TUMOR_BAM           #from preprocessing steps 
--enable-map-align false

In upcoming software releases, it will be possible to calculate MSI in Tumor/Only mode even while running a Tumor/Normal workflow, thus eliminating the need for an additional analysis.