How to calculate IBD

Question

[cetin.m]

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?

Answer 1

[Charles Warden]

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).