I have a set of biological replicates consisting of multiple normal and tumor mouse samples. The samples are not matched (each sample corresponds to a different animal) but these are all mice from the same litter and are supposed to be genetically identical (apart from the somatic mutations in tumors).

I am interested in a pipeline that would produce joint analysis of all samples. All the pipelines/tutorials I've seen are about single tumor/normal pairs. In theory, these can be re-used for multiple replicates by looking at overlapping mutations. But this seems to me to be a bit primitive. Also, in my case the samples are not matched so maybe it makes sense to consider some sort of cohort/pooled analysis.

I am facing such an experimental design for the first time so would welcome any suggestions.