Here my next problem:
Is there an easy way to get the latest individual genotypes for the HapMap (These samples from the HapMap project. The id starts usually with NA...) samples?
I tried several things but without any success.
Here a list of tools I used:
BiomaRt and R, HapMap Browser, Ensembl...
What they have in common is that some individuals or genotypes are missing or it's an old hg release or it's even impossible. The combination of the HapMap and the 1000G data would be nice.
My goal is a simple genotype Matrix, like this:
It doesn't matter which code. Binary or Bases, etc.
And is there a good answer why this is such a hard task? Especially the combination of HapMap and 1000G data?