Hello,
Is there a way to turn off the initial summary statistics calculated and displayed by SNPTEST (snptest_v2.5-beta4)? I have a sample file with tens of thousands of continuous phenotypes (expression data). When I specify a single phenotype (-pheno) to run an association test on, the summary statistics for all phenotypes in the sample file are still reported. As an example, the sample file with all phenotypes take 45min to complete, but a sample file with only the tested phenotype takes 4min to complete. It's easy enough to create custom sample files for each run (cut -f1-6,x) but I was wondering if there was an option so I wouldn't have to do so.
Any help would be appreciated.