I work with data containing SNP genotypes for thousands of individuals. One of the task I had was to perform IBD between the individuals to find out the individual relatedness. I perform the IBD analysis with PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/ibdibs.shtml).
However, I always wondered how it works mathematically in a concrete way. I tried to find out on internet, but all I get is theoretically informations but not how you practically estimate the IBD parameters.
So, maybe someone here can explain it to me?
For example, let say I want to find out the relatedness between individual 1 and 2 with SNP genotypes:
Ind1: A/G A/A G/C T/G T/T
Ind2: A/G A/G G/G T/G A/T
How do I estimate the IBD given those genotypes between Ind1 and Ind2? Thanks!
