I’ve been having some fun with my daughter’s personal genomics. You see, she has her whole pedigree out to r = 1/4. So, for example, contributions from her grandparents seem to be about on this order:
Paternal grandfather = 0.28
Paternal grandmother = 0.22
Maternal grandfather = 0.23
Maternal grandmother = 0.27
I’ve also calculated the number of recombinations which occurred leading up to the gametes which fused to create her. That will be for a future post. But here let’s confirm that she is not inbred. I used plink for this. Here is the description of the command:
Given a large number of SNPs, in a homogeneous sample, it is possible to calculate inbreeding coefficients (i.e. based on the observed versus expected number of homozygous genotypes).
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The estimate of F can sometimes be negative. Often this will just reflect random sampling error, but a result that is strongly negative (i.e. an individual has fewer homozygotes than one would expect by chance at the genome-wide level) can reflect other factors, e.g. sample contamination events perhaps.
My main confusion here was which population I should select? Should I select GIH (HapMap Gujaratis?) or CEU (Utah whites)? I ended up on the TSI sample (Tuscans) as …