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 BAM 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. 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 to create the collapsed BAM in the preprocessing step. Use v1.1.0 of the microsatellite list.

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.

DRAGEN command-line recipe

/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                      #path to DRAGEN linear hashtable                
--output-directory $OUTPUT   
--output-file-prefix $PREFIX 
--tumor-bam-input $TUMOR_BAM            #from preprocessing steps 
--enable-map-align false

BSSH Somatic App

Follow the BSSH variant calling instructions (Phase 2) with the following changes:

Configuration

• Somatic CNV Calling—Select Tumor-only

• Input BAM—Select the tumor BAM and the Sample Sex to Unknown. Click Add a New Row to input another tumor sample. Each tumor BAM is entered as a new row.

• Systematic Noise Filter—uncheck Enable Systematic Noise Filter.

• CNV Baseline—None

Biomarkers

• View the Biomarkers options by clicking on + Biomarkers

• Microsatellite Instability—check Enable MSI calling

• MSI References—navigate to the Project containing the reference directory of *microsat_normal.dist files that match the reference genome used.

• Custom MSI Regions—navigate to the *.tsv file containing the microsatellite list file that matches the reference genome used.

Advanced Settings

• View the Advanced Settings options by clicking on + Advanced Settings

• Enable Duplicate Marking—Uncheck this setting

• Enable Variant Calling—Uncheck this setting

• Enable Common Germline Variant Tagging—Uncheck this setting

• Enable Multi-allelic Filtering—Uncheck this setting

Additional Arguments

• Check the acknowledge and agree box

• In Additional DRAGEN Command-line Arguments, add --enable-cnv false

ICA

Follow the ICA variant calling instructions (Phase 2) with the following changes:

Input Files

• Enter the Tumor BAM File for tumor sample(s)

• Enter the Tumor BAM Index for the tumor sample(s)

• Systematic Noise BED File—Do not select

• CNV Files—Do not select

• Microsatellites File—navigate to the *.list file containing the microsatellite list file that matches the reference genome used.

• Microsatellites Normal References Directory—navigate to the directory of *microsat_normal.dist files that match the reference genome used.

Variant Calling Options

• Enable Small Variant Caller—false

• Enable Germline Tagging—false

Targeted Callers

• MSI Command—tumor-only

• MSI Coverage Threshold—60

• Enable Tumor Mutational Burden—false

Variant Annotation Options

Enable Variant Annotation—false