What is the difference between MSIsensor2 and the previous MSIsensor ?

MSIsensor2 is an improved version of MSIsensor, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only or Cell-Free Tumor DNA (ctDNA) sequencing data. The original MSIsensor is specially designed for tumor/normal paired sequencing data.


Can you give a example about parameters while running MSIsensor2 tumor only module?
$ msisensor2 msi –M models_hg38_1000genes -t Sample.tumor.bam -o output.tumor.prefix

Note: tumor bam index files are needed in the same directory as bam files and each bam file must be aligned with hg38/GRCh38.

Can you give a detailed description of the output?
If you follow the command above, your will get 3 files for each sample.
  • output.tumor.prefix : msi score output
  • output.tumor.prefix_dis : read count distribution ( T: tumor)
  • output.tumor.prefix_somatic : somatic sites detected