Hi everyone, I am new to bioinformatics field. So please apologize for my questions that I am not unaware of. I wanted to use a tool called Clove https://github.com/PapenfussLab/clove to classify the breakpoint calls from the gridss software (https://github.com/PapenfussLab/gridss) as Structural variants. But for using Clove I need to specify two values 1. Mean coverage value. 2. Variance of coverage value.
So is there a method or tool where I can calculate these values from my bam File. It would be really helpful if you can answer.