Please take a look at the FaST-LMM-Select section of the documentation to understand more fully.
The reason you want to select the SNPs for the similarity matrix is reduce the noise and pull out a more of the signal for the snp of interest.
You can run with everything in the similarity matrix, but your prediction accuracy improves when you remove 'unrelated' noise.
The reason you want to select the SNPs for the similarity matrix is reduce the noise and pull out a more of the signal for the snp of interest.
You can run with everything in the similarity matrix, but your prediction accuracy improves when you remove 'unrelated' noise.