Step 2. Isolate Data of Interest

Figure 1. Inactivate rows

Figure 2. Rename subset spreadsheet

Next, you need to isolate the SNPs that do not meet your quality control standards. For this example we use a minor allele frequency threshold of 0.10, and a call rate threshold of 0.965.

From the Marker Statistics spreadsheet sort ascending the Minor Allele Freq. column (Left Click > Sort Ascending) and inactivate all rows where the minor allele frequency is above 0.10 (Figure 1).

Next, create a row subset spreadsheet (>Edit >Row >Subset Spreadsheet). A new spreadsheet will be created with a list of SNPs below the minor allele frequency threshold. Rename the subset spreadsheet in the project navigator MAF < .10 (Figure 2).

Return to the Marker Statistics spreadsheet and activate all rows (>Edit >Row >Activate All).

Now perform the same workflow for call rates by sort ascending the Call Rate column, inactivating all rows with a call rate below 0.965, and creating a row subset spreadsheet.

In Figure 2 this is the Call Rate < .965 child node.