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README.md

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 MSIsensor
 ===========
-MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. Given paired tumor and normal sequence data, it builds a distribution for expected (normal) and observed (tumor) lengths of repeated sequence per microsatellite, and compares them using Pearson's Chi-Squared Test. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data. Since there are many users complained that they don't have paired normal sequence data or related normal sequence data can be used to build a paired normal control, we released MSIsensor V0.3. Given tumor only sequence data, it uses comentropy theory and figures out a comentropy value for a distribution per microsatellite. Our test results show that it's performance is comparable with paired tumor and normal sequence data input(figure below). We suggest msi score cutoff 11% for tumor only data. (msi high: msi score >= 11%).
+MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. Given paired tumor and normal sequence data, it builds a distribution for expected (normal) and observed (tumor) lengths of repeated sequence per microsatellite, and compares them using Pearson's Chi-Squared Test. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data. Since there are many users complained that they don't have paired normal sequence data or related normal sequence data can be used to build a paired normal control, we released MSIsensor V0.4. Given tumor only sequence data, it uses comentropy theory and figures out a comentropy value for a distribution per microsatellite. Our test results show that it's performance is comparable with paired tumor and normal sequence data input(figure below). We suggest msi score cutoff 11% for tumor only data. (msi high: msi score >= 11%).
 
 ![](https://github.com/ding-lab/msisensor/blob/master/test/tumor_only_vs_pair.jpg)