I would like to analyse the association of few SNPs with phenotypes and summarize if those SNPs may cause increased risk or normal risk for assumed phenotypes. In brief, I would like to genotype SNPs, obtain the list of SNPs identified in specimens and analyse the meaning of those SNPs. I read a lot of articles about it as well as familiarized with GWAS, however I still do not know how to perform the last part of the study - association of the SNP with phenotype. In some source I found the method described (they performed something like I'd like to), however it is unclear for me how to reproduce those steps. And here I'd like to ask for your help.
They wrote "The outcomes for each phenotype are calculated based on cut off reporting thresholds, which are set based on the negative log of p-value for the strongest SNP GWAS-associations (high) and the weakest SNP associations (low). Then, combined SNP weight for each phenotype is calculated based on aggregation of all individual SNP weights, which are statistically significant from published GWAS studies and SNPs ranking on aggregated public databases (Phenotype-Genotype Integrator@NCBI)".
My questions are: 1. Is there any software, which performs such analysis and is just not mentioned above? 2. If not, how to set thresholds and find the strongest and the weakest SNP associations based on my data? 3. How to aggregate properly weights of all SNPs? 4. How to obtain the aggregation of SNP weights fro mentioned public databases? 5. Is the mentioned above method in general correct for analysing the association of SNPs with phenotype?
I would very appreciate if you help me with that as I am not so familiar with such methods.