Hello,
I am trying to measure how many SNPS were actually called for each individual in my dataset.
Our individuals were genotyped using the [Human Orgins Array]. This array genotypes about ~629,000 SNPs known to be relevant to population genetics. I was using the PLINK --missing command to calculate levels of missing SNPs in our dataset. However I am not sure if this command accounts for the fact that some SNPs are not missing but were purposefully not chosen by the array.
So I wanted to use the obligatory missing PLINK command but I do not really understand how to get the test.oblig which states which SNPs are missing for which clusters. Nor do i understand the difference between that file and the test.zero file. Any guidance would be much appreciated.
Thanks
