The tool Generate MSI Baseline can be used to generate MSI baseline tracks. To do so, go to:
Tools | QIAseq Panel Expert Tools | QIAseq DNA Panel Expert Tools () | Generate MSI Baseline (beta) ()
First select one or more mapped reads as inputs. You can then specify a microsatellite loci track and set up the parameters seen on figure 3.30.
You can change the Flanking signature length that is set by default at 8. You can also choose to allow one mismatch, or none at all when deselecting this option. Finally, you can choose to ignore broken pairs.
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 alternaltive analysis set) reference sequence.