Step 3. Deactivate Columns by Row Labels

Now that you have isolated the markers that do not meet your quality control thresholds, you can run a simple script from your original spreadsheet to filter these from analysis.

From your original spreadsheet, select >Edit >Deactivate Columns By Row Label (Figure 1), and choose the spreadsheet with the list of markers with minor allele frequencies < 0.10. This will deactivate those markers in your spreadsheet.

Figure 1. Deactivate columns

Run this script a second time, and choose the Call Rate < 0.965 spreadsheet. This will deactivate any markers that did not meet the call rate threshold.

At this point any further analysis will not take these "poor quality" markers into consideration. However, it is often a good idea to create another column subset spreadsheet with only the "good" markers. To do this, run >Edit >Column >Subset spreadsheet again. This will ensure those markers are not used in future analyses.