Tuesday, 28 October 2008

genetics - What is the frequency of double-hets between parent and child?

Say both parent and child are genotyped for all SNPs. In this setup we are only looking at variant positions between one parent and child - so neither parent nor child are homozygous reference (no AA/AA) in the millions of positions we are studying.



Assume all variants are biallelic and there is no de novo mutation (no AA/BB or BB/AA)



P    C
AA AB
AB AA
AB AB
AB BB
BB AB
BB BB


What is the fraction of AB/AB among these possibilites?



We are looking at all positions in the genome so the minor allele frequency (MAF) of B allele varies. You can choose whatever B frequency you like.

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