I am running Snptest on 2 datasets together. I used the -overlap option to make sure I tested only the SNPs common to both datasets. My code looks as follows:
/apps/snptest/2.5.2/snptest_v2.5.2 \ -data data1.imputed pheno1.sample data2.imputed pheno2.sample \ -overlap \ -o combined.snptest \ -frequentist 1 \ -method score \ -pheno pheno \ -cov_names cov1 cov2 cov3 cov4 \ -exclude_samples all_samples_exclusions_for_snptest.txt \ -exclude_snps exclude_snps.txt
Snptest documentation mentions about the -overlap option: "A restriction is that all .gen files must have SNPs in strictly increasing order of position (after SNP exclusions). If this is not the case a warning will be given." https://mathgen.stats.ox.ac.uk/genetics_software/snptest/old/snptest_v2.3.0.html
I'm trying to check whether I have add such a warning, has anyone got an example of how such a warning might look like? I want to be absolutely sure I haven't missed it.