We got some SNP chip data from PLINK (bed, bim, fam files) of two different genotypes. We also have the proteomics expression matrices for these data sets.

I was wondering if there is a tool or a workflow we can follow, which will help us analyzing the data.

I am new to GWAS and pQTL and would like to understand how it should be analyzed. i have found multiple papers about this topic, but none of them are sharing their code.

Until now I have done the pre-imputation preparations and the imputation using the sanger Inputation server. I have also done the post-imputation QC. But I am not sure how to proceed.

The next steps I would help with are as follow:

1. LD pruning to find independent SNPs
2. determine the additive effects of each SNP on the protein expression (linear regression model)
3. principal component analysis of specific phenotypes (e.g. gender, age, etc.). 4 ...

I'm not sure really sure how to continue though. I know it can be done in PLINK, but can anyone help me understanding it?

thanks

Assa

P.S.

Did I miss something?