Generate MSI Baseline

The tool Generate MSI Baseline can be used to generate microsatellite instability (MSI) baseline tracks. The tool can be found in the Toolbox:

        Toolbox | Biomedical Genomics Analysis (Image biomedical_folder_closed_16_n_p) | Oncology Score Estimation (Image oncology_tools_folder_closed_16_h_p) | Generate MSI Baseline (Image msi_baseline_16_h_p)

To generate a baseline, select at least five read mappings from microsatellite stable (MSS) samples as input. For better results, we recommend using 15 samples or more.

In the next step, the following parameters can be adjusted (figure 8.7):

See Detect MSI Status for more details about how the length of a locus is determined.

Image generatemsi
Figure 8.7: Parameters for Generate MSI Baseline.

Note that all the MSI baseline tracks available in the QIAseq TMB Panels hg38 Reference Data Set have been generated from samples that were mapped against the hg38 (no alternative analysis set) reference sequence.