How to filter for or exclude a list of a large number of SNPs in GenomeStudio

In the following example, a list of 27 SNPs from GSA-24v3-0_A2 manifest will be selected and displayed in GenomeStudio full table data, while excluding all the remaining SNPs (654,000); or vice versa, the list of the 27 SNPs will be excluded, and the remaining 654,000 SNPs displayed.

1. Select the SNPs of interest from the manifest file (csv format). Select the SNPs according to the “Name” header, not the “IlmnID” header, as shown in the screenshots below.

1. Generate a .txt file (tab delimited text file) with two columns:

• Insert the selected SNP names into the first column of an empty excel sheet. Label the header of the first column: “Name”.

• Label the header of the second column with any name that is not a name that already exists in the GenomeStudio table, to which the column will be imported. In the following example, the second column will be named: XXXXX. Assign to all SNPs the same number or letter. In the current example all SNPs will be assigned the number 1.

• Save the excel sheet as a tab delimited text file (.txt format) then close it. It is important to close the file, otherwise it cannot be imported into GenomeStudio.

1. Import the created .txt file into the GenomeStudio full table data:

   1. Select the icon for ‘Import Columns’ (left arrow symbol) in the GenomeStudio full data table.

1. 2. Browse to the folder location where the generated txt file is saved, choose the file, and select OK.

1. 3. The second column of the generated txt file is now imported into GenomeStudio data table, each cell (here each has number 1) assigned to the corresponding SNP name.

1. Filter the GenomeStudio table for the SNPs that have been assigned number 1 (in this example), according to instructions for “Filtering Rows” on page 38 of GenomeStudio 2008.1 Framework User Guide, and as shown in the screenshots below.

Only the SNPs of interest are now displayed in GenomeStudio table.

1. Alternatively, exclude the SNPs list (that have been assigned number 1 in this example) from the GenomeStudio table, by selecting the Not checkbox in the Filter Table Rows window, as shown in the screenshot below.

The selected SNPs of interest are now excluded from the GenomeStudio table.

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