I am trying to understand how IBD calculations are done based on SNPs. I haven't been able to grasp the subject even though I looked at several papers.
I am hoping by looking at a simple case someone could show me how it is done.
Assume there is a locus and two individuals. They may or may not be related, which we are trying to find out.
Ind1: 0/1
Ind2: 0/0
What is the IBD between these two?
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written
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cetin.m
1 answer
I would say you need more markers, even for an example.
I would be interested in knowing about additional tutorials on the subject, but I think plink has a IBD decent calculation (and you can see what is the effect of LD pruning).
If you do things like plot IBD for technical/biological replicates from the same individual (versus parent-child pairs), you should be able to see a clear difference in range of values (and get some rough idea about the range of accuracy for those calculations).
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