# 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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-bee264731cdff1385e76b94b499ddd275333f374%2Fimage1.jpg?alt=media\&token=e16f0ad4-0d5e-4e06-bb3b-b75ecd1c0c52)\
![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-ee6b3db79451d2265cfc0d3d1bd00314ec466e0c%2Fimage2.jpg?alt=media\&token=561af99a-3df3-4a9a-a836-83c114c36f26)

2. **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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-84786d9edf9f83f4d6eaa79f8635292bd85ca2b7%2Fimage3.jpg?alt=media)

3. **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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-351d6db754f64dfe1a86fa7c952bc54e95ba12f0%2Fimage4.jpg?alt=media)

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

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-86dacc8404af7b372a181da35286b717f033bbbc%2Fimage5.jpg?alt=media)

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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-eafb54adf079264f538d0a64aa5824344e9f765b%2Fimage6.jpg?alt=media)

4. **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](https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/genomestudio/genomestudio-2-0/genomestudio-2008-1-framework-user-guide-11318815-a.pdf), and as shown in the screenshots below.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-7b803d04fe5ae83af073e5644c098c8fcbfc702b%2Fimage7.jpg?alt=media)

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-418e2f02f41bc269712daa62ca3ae8aada41614d%2Fimage8.jpg?alt=media)

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

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-1c573333620c5f1ecf61e3c7e52614bfbac2aa50%2Fimage9.jpg?alt=media)

5. **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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-241259943fa60c7c54a2a6819221de3c46330b84%2Fimage10.jpg?alt=media)\
**The selected SNPs of interest are now excluded from the GenomeStudio table.**

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-b6540518a089171f10ab89b4dd5bcf5fe4031ff1%2Fimage11.jpg?alt=media)

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