I am conducting a genomewide methylation QTL study. This entails 2M (methylation markers) * 650K (SNPs) tests, which is intractable on our cluster. Thus, we want to reduce the number of SNPs using only a subsample of approximately independent (tag) SNPs. The Tagger server and Haploview crash when I upload the Plink format GWAS data, so I wonder if perhaps Tagger is not well-suited for operations including so many SNPs? Is this the case, or am I making an error otherwise? If Tagger is not appropriate for this task, could you recommend another tool?