Viewing the prepared input

Click on the eye icon to examine the prepared composite dataset. The results are in the "admix.ped" and "admix.map" files. The most important thing to note is the number of SNPs that passed the filter. We want this to be at least 100,000, so once again it is fine. If we had used a minimum coverage parameter that was too stringent, we would need to rerun the Prepare Input tool with a lower value before continuing.