It's been a few years (decades) since my last class in population genetics, so I require guidance. We have WGS from 16 individuals of an inbred mouse line and have performed joint variant calling with the GATK pipeline. We would like to determine the degree of genetic diversity in the strain, with a particular emphasis on sensitivity/detection limits. Specifically, we'd like to know something along the lines of "given 20X coverage of 16 individuals (= 10X coverage of 32 chromosomes), we identified XX variants, of which YY had an allele frequency of 3% (present on only one chromosome). The estimated total number of variants present at this allele frequency is ZZ." Recommendations for tools to help in our analysis would be appreciated.
EDIT: We've settled on VCFtools for most metrics of genetic diversity (e.g., Fst estimate, HW equilibrium, etc), but are still open to suggestions for calculating sensitivity/detection limits per our original post.