Standardizing genotype (risk prediction)

[choishingwan]

When trying to perform risk prediction, we need to compute the standardized genotype. However, if there is no variation in the sample (e.g. all sample has the same genotype), we cannot standardize them as the SD = 0.

Currently we just set the genotype to 0. A better way might be to pre-filter those genotype just like what we've done with the LD matrix. Which one is better?