You can use MSIsensor
- tool : https://github.com/ding-lab/msisensor
- article : https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt755
Tumor only mode :
# first scan genome of interest msisensor scan -d reference.fa -o microsatellites.list # Then use tumor bam file to detect MSI msisensor msi -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix
Hi, Output of a tumor only case, is 2144 3491 15.01. I have a few queries regarding it.
1.From the sample output given on the github page, I understand that 15.01 is the % of "Number of somatic sites" and is the msi score as well. Is it msi-high or msi-low? 2. What is the cutoff score? Because it is mentioned that the cutoff values are calculated for various cancer types. 3.How do I get the MSI status?