e it accounts for differences in read depth between the tumor and normal sample. Varscan 2 can also be used for identifying copy number alterations in tumor-normal pairs.
- <a href="https://bioinformatics.mdanderson.org/public-software/muse/">MuSE</a> This is a beneficial mutation calling tool when you have both tumor and normal datasets. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1029-6">The Markov Substitution Model for Evolution</a> utilized in this tool models the evolu