Virtual Variants
The virtual variant feature allows you to add new variants to a case, either to refine the boundaries of a variant you have reviewed in IGV or to create a single variant that overlaps separate adjacent variant calls.
Virtual variants are listed in the grid in purple text. Grid data contain only annotation information. The call details and metrics are available only for the original calls, which are listed in the grid without modification.
For information about viewing data in IGV, see IGV Visualizations.
NOTE
The virtual variant feature only supports creating and modifying CNVs. Other variant types are not supported at this time.
Create a Virtual Variant
| 1. | In the variant grid, select the IGV column icon for a variant call you want to use as the basis for a virtual variant. |
| 2. | In the IGV viewer, select Create Virtual Variant. |
The IGV viewer highlights the range for the selected variant and lists the start and end locations in the Positions field.
| 3. | Click on the locations of the start or end positions of the virtual variant, and then select one of the following options from the dialog box. |
| • | To set a new start position, select Move Start Marker. |
| • | To set a new end position, select Move End Marker. |
| 4. | For each subject, enter the number of copies. |
| 5. | Select Create. |
TruSight Software converts the selected range into a single annotated variant and lists the new virtual variant in the grid.
NOTE
TruSight Software may take several minutes to generate the virtual variant.
View Virtual Variants
Virtual variants appear in purple text in the grid, with the variant type noted as virtual variant.
To view virtual variants and the CNV calls they overlap, do as follows.
| 1. | Select the variant grid Linked column drop-down arrow for a virtual variant or a called variant that is associated with a virtual variant, and then select Show Virtual Variants. |
| 2. | To remove the filter, select Close View. |