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 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.

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