If you want to focus on variants that differ between the two tracks, the order in which the two samples are selected matters, as the tool will not combine the variants in the two tracks, but will filter out one. This is illustrated in figure 27.57.
To run the tool:
Toolbox | Resequencing () | Compare Variants | Compare Sample Variant Tracks
In the first step of the dialog, you select the variant track that should be taken as input. Clicking Next shows the dialog in figure 27.58.
At the top, select the comparison track. Below, you can choose whether the result should be the variants from the input that match the comparison track, or whether it should be the variants that are different from the variant track. The match criterion here is an exact match on the position and allele sequence.