9.3. How can I get amino acid prediction information for the variants in my data?
The Workbench offers two different ways of viewing mapping data - the Stand-alone view and Tracks.
If you work with the Stand-alone view, all the relevant information for looking for sites of a potential amino acid change is included within the mapping object itself. In this case we can predict the amino acid changes based on the CDS annotations contained in the mapping object, and thus this information is then included in the annotated (variant) table.
If you on the other hand work with tracks each type of data has it own track. For example, reference sequences are held in a different track than CDS annotations, which are in their own track. Similarly, gene annotations are in a single track variations are in a single track, and so on. Since in this case the mapping data and the CDS annotations are held in two different objects, a second step is needed in order to find and output sites of potential amino acid changes.
This additional step is to run the Amino Acid Changes analysis tool, which can be found here:
Toolbox | Resequencing | Functional Consequences | Amino Acid Changes
How to use the tool is described in the manual following the link below:
Please note that if you start with a stand-alone mapping object and choose to output to both a track and table output type, then the table output will contain the amino acid change information but the track-based output will not. This is for consistency. If you wish to get a track containing both the variant information and the amino acid change information, please just run the Amino Acid Changes analysis tool, as suggested above.