After providing answers to over 100 questions here, I now have one of my own. Actually, this is a two-part question. What tool(s) do you use to calculate genetic heterogeneity from SNP genotype data collected across an entire chromosome or genome? If the measure of heterogeneity is at or near zero, then the individual (human, animal, plant) is a product of inbreeding. This number will rise as the parents come from increasingly divergent genetic backgrounds.
That then brings up the second part of the question. For those of you who have looked into such measures of genetic diversity or heterogeneity, how useful is this and what kinds of values can I expect from the human genome-wide SNP genotypes I have? A preliminary and crude analysis gave me 69% of SNPs across chromosome 7 as homozygous, but that value rises to 92+% across two small HLA loci. That seems interesting but I don't know where to go with this.
Thanks in advance for any insight, advice.