I doing an eQTL analysis, but I am a bit struggling with the proper correctinng for multiple test because of the massive amount of tests performed. I have more or less 400,000 SNPs and 20,000 transcripts expressed. I am performing a basic analysis using PLINK (Yes I know that there are more newer programs available like matrixEQTL etc, but unfortunately it was decided for me that I have to use PLINK). So for trans eQTLs the amount of tests = 400000*20000=8.00E+009 test so a massive amount and bonferroni correction would be 6.25E-012, but it is debated that this is too conservative. For cis (500kb up or down stream of the transcript) I dont really know what the correct way is of determining the proper cut off, some people mentioned that just taking the GWAS whole genome significance (about 2E-08) level would be appropriate but I am not sure about this. In plink there is the option --adjust to calculate adjusted p-values, but I split up the chromosomes in PLINK analysis otherwise the analysis takes almost a month. So I was hoping to find something to calculate corrected p-values afterwards or just a good way to find a proper cut off value, does anyone has a good idea?