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MSIsensor specifications


Unique identifier OMICS_02192
Name MSIsensor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data The list of microsatellites, the msi score output, the read count distribution, the somatic sites detected and the germline sites detected.
Operating system Unix/Linux
Programming languages C++
License MIT License
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes




No version available



  • person_outline Li Ding
  • person_outline Kai Ye

Publication for MSIsensor

MSIsensor citations


Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] cant drops of coverage. As the reference set, we pooled all germline samples obtained from the same batch of the respective tumor sample. Potential microsatellite-instability (MSI) was assessed using MSIsensor with default settings.Sequential samples were compared in a pair-wise fashion: sample at F/U vs. sample at diagnosis. Estimations of cellular prevalences and clustering of mutated population […]


Multilevel genomics of colorectal cancers with microsatellite instability—clinical impact of JAK1 mutations and consensus molecular subtype 1

Genome Med
PMCID: 5442873
PMID: 28539123
DOI: 10.1186/s13073-017-0434-0

[…] The level of MSI per sample was estimated from the exome sequencing data using the algorithm MSIsensor [] with default settings. For a catalogue of microsatellites in the reference genome (homopolymers of a minimum of 5 base pairs and microsatellites with maximum repeat unit length 5), the nu […]


Identification of neutral tumor evolution across cancer types

Nat Genet
PMCID: 4934603
PMID: 26780609
DOI: 10.1038/ng.3489
call_split See protocol

[…] supporting the variant. Non-CRCs in the TCGA had mutations called using Mutect according to the pipeline described in ref. Microsatellite instability in the TCGA colon cancer samples was called using MSIsensor. Annotation was performed with ANNOVAR.To fit the neutral model to allele frequency data we considered only variants with allele frequency in the range [fmax,fmin] corresponding to [t0,t] in […]


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MSIsensor institution(s)
Departments of Genetics and Mathematics, The Genome Institute, Washington University in St. Louis, MO, USA; Department of Genetics, Division of Statistical Genomics, Washington University in St. Louis, MO, USA; Department of Medicine, Washington University in St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, MO, USA
MSIsensor funding source(s)
Supported by National Human Genome Research Institute (U01HG006517) and National Cancer Institute (R01CA180006).

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