To add a custom field to variant tables and panes
You can combine multiple fields in a reference database to create a custom field, and then add the custom field and its value to the Variant pane and the Variants pane on the Sample Variant Data sub-tab on the Sample tab. When you select a reference database field to use for creating a custom field, if the field contains multiple values, then you can select only a single value from the field. For example, the Allele Frequency (AF) field in the ExAC Reference database contains a frequency value for the variant nucleotide and a frequency value for the reference nucleotide. If you select the AF field, then you must select either the frequency value for the variant nucleotide or the frequency value for the reference nucleotide. You cannot select both values.
1. If you have not done so already, do one of the following to open the Variant tab:
• Double-click a variant on the Variants sub-tab on the Patient tab.
• Double-click a variant on the Variant sub-tab on the Panel Statistics tab.
• Right-click a variant on the Sample Variant Data sub-tab on the Sample tab, and on the context menu that opens, select Variant Details.
• Double-click a variant on the Sample Variant Data sub-tab on the Sample tab.
2. Right-click in a Reference pane, and on the context menu that opens, click Add Values to Variant Table.
The Add Values to Variant Table dialog box opens. The dialog box lists all the fields in the selected Reference database. It also provides a description of the value that is contained in each field.
3. Do one of the following to select a field:
• Double-click the field.
• Right-click the field, and on the context menu that opens, click Add Value(s).
The Field Configuration dialog box opens. You use the options on the dialog box to specify the field value that you are using for the custom formula.
4. Select the value in the field that you are using in the formula for the custom field. The value that is selected by default is determined by how the field is defined in the VCF file for the database.
Value | Description and Options |
|---|---|
R (one value for each possible allele including the reference) | The field contains multiple values, with one value for each possible allele, including the reference allele. Therefore, the values that you can select are the following: • Matching Alt allele - Add the value only for the matching alternate allele (single value) • Ref allele - Add the value only for the reference allele (single value) |
A (one value per alternate allele | The field can contain multiple values, with one value for each alternate allele. Therefore, the values that you can select are the following: • All alt alleles - Add all values for all alternate alleles (A single value if only one alternate allele exists; however, multiple values possible if more than one alternate allele exists) • Match Alt allele - Add the value only for the matching alternate allele (single value) |
Fixed Value | • Fixed - Add only the specified number of fixed values specified value - 1 for the first value, 2 for the second, and so on. |
. (number of possible values varies, is unknown, or is unfounded) | Based on different variants, the number of values in the field can vary. |
5. Click OK.
 | After you select the value that you are adding, the following happens: • A tab that is named the same as the selected field, a Field tab, opens below the list of available fields. • A preview of the selected field and its value is displayed in the Work area of the dialog box (the blank area below the Field tab). • A preview of the selected field and its value is also displayed in the Preview pane (the bottom pane of the dialog box). |
6. Do one of the following:
• Click in the Add Text field, enter the needed text (for example, if you are creating a field to show a ratio, you might select a forward slash), and then click Add Text.
The text is displayed on the Field tab and in the Work Area and the Preview pane.
• To create a formula, select Formula, and then select the operator for the formula. Parentheses are also available for setting the order of operations in the formula.
As you create the formula, the following happens:
• A preview of the formula, including the selected fields, their values, and the operators, is displayed on the Field tab and in the Work area of the dialog box (the blank area below the tabs).
• The Preview pane displays the current value for the formula.
| | If you add a field, a text separator, or an operator in error, then right-click it in the Work Area, and on the context menu that opens, click Remove. |
As you select multiple fields for the custom field, the display on the Field tab and in the Work Area and the Preview pane are dynamically updated.
8. Optionally, to add another custom field, click the (+) tab to open a new blank tab, and then repeat Step 3 through Step 7. Repeat these steps as many times as needed to add all the necessary custom fields.
9. Optionally, to change the name of the Field tab, select the tab to make it the active tab, and then in the Column Name field, enter a new name for the tab.
10. Click OK.
The Field Configuration dialog box closes. The Add Values to Variant Table dialog box remains open.
11. Click OK on the Add Values to Variant Table dialog box.
The custom fields are added to the various variant tables and panes. The dialog box closes. The Variant tab remains open.