Common bioinformatics tools required to analyze the mutational distribution in mice genomes

Question

[Gene_MMP8]

I have 21 normal-tumour matched whole-genome sequencing data from isogenic mice samples. I intend to perform the following:

1. Distribution of substitutions, indels, rearrangements and copy number changes across samples.
2. Mutational signature analysis of the samples.

I am aware of tools such as SIFT, VEP etc that can take care of the distribution of substitutions. But can you suggest me some tools for the other analyses? (indels, rearranagements, copy number changes and mutational signature analysis)