I read many explanations about LD but I’m still not comfortable with the explanations.
as you can see on these videos, most of them explains as if LD is about the relation between the genotype frequency of parental cell and gametes made from it. But if so, I should have the genotype frequency of the parental cell and the frequency for all the gametes made which is impossible.
Or is it’s the relation between the genotype frequency for each loci(such as 0.6 for A and 0.4 for a in one loci and 0.6 for B and 0.4 for b in another loci) of the parental population and the combined genotype frequency of the sibling population(such as 0.36 for AB , 0.16 for ab)? if so, isn’t it also impossible to get the frequency of the parental population?
I suppose I’m not getting it right I’m so confused.
For my situation, if I look at the VCF file I made, I have genotypes of 0|0 1|0 0|1 1|1 for each SNP.
For simplicity, if there are two samples(A and B) and I want to see how linked two SNP positions 1,2 are,
how do I find out?
let’s say sample A SNP position 1 has a genotype of 0|0 and position 2 has a genotype of 1|0.
and sample B SNP position 1 has a genotype of 0|1 and position 2 has a genotype of 1|1
is it possible to calculate the linked relationship? or are there other values required.
Please help me
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