To add fields from a reference database to variant tables and panes
You can add fields from a reference database to the Variant pane and the Variants pane on the Sample Variant Data sub-tab on the Sample tab. Fields in the reference database can contain single values, or they can contain multiple values. 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. Depending on the options that you specify, the field can be added with a just a single value (for example, the value for just the variant nucleotide), or the field can be added with multiple values (the values for both the variant nucleotide and the reference nucleotide).
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 the appropriate reference information pane, for example, the ExAC Data 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 which values in the selected field are to be added to the various variant panes and tables.
4. Select the values in the field that are to be added to the various panes and tables. 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. • All alleles - Add all values for all possible alleles (multiple values) • 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. • All alt alleles - Add all values for all alternate alleles (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 | • All - Add all values (multiple values) • 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.
The Field Configuration dialog box closes. The Add Values to Variant Table dialog box remains open.
 | After you select the values that are to be added, 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 values 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 values is also displayed in the Preview pane (the bottom pane of the dialog box). |
6. Optionally, to change the name of a Field tab, select the tab to make it the active tab, and then in the Column Name field, enter a new name.
| | If you add a field in error, then right-click it in the Work Area, and on the context menu that opens, click Remove. |
7. Optionally, to add another field, click the (+) tab to open a new blank Field tab, and then repeat Step 3 through Step 6 to add the field to the various panes and tables for the selected variant. Repeat these steps as many times as needed to add all the necessary fields.
8. Click OK on the Add Values to Variant Table dialog box.
The selected field is added to the various variant tables and panes. The dialog box closes. The Variant tab remains open.