This tool removes orphan variants from a variant track. Orphan variants are described as lacking a variant allele, i.e., a corresponding non-reference variant with exactly the same start and end positions.
To start the tool, go to:
Toolbox | Resequencing Analysis | Variant Filtering | Remove Orphan Reference Variants
In the first dialog, select the variant track from which you would like to remove orphan variants, and click Next to decide whether to Save or Open the resulting variant track.