Output from the Annotate Variants (WES) workflow
The output generated are:
- Filtered Annotated Variant Track (
) Hold the mouse over one of the variants or right-clicking on the variant. A tooltip will appear with detailed information about the variant.
- An Amino Acid Track Shows the consequences of the variants at the amino acid level in the context of the original amino acid sequence. A variant introducing a stop mutation is illustrated with a red amino acid.
- Genome Browser View Annotated Variants (
) A collection of tracks presented together. Shows the annotated variant track together with the human reference sequence, genes, transcripts, coding regions, and variants detected in dbSNP Common, ClinVar, 1000 Genomes, and PhastCons conservation scores (see figure 19.5).
Figure 19.5: The output from the Annotate Variants template workflow is a track list containing individual tracks for all added annotations.
It is possible to add tracks to the Genome Browser View by dragging the track directly from the Navigation Area to the Genome Browser View. On the other hand, if you delete the annotated variant track, this track will also disappear from the Genome Browser View.
Open the annotated track as a table (see figure 19.6). The table and the Genome Browser View are linked; if you click on an entry in the table, this particular position in the genome will automatically be brought into focus in the Genome Browser View.
Figure 19.6: The output from the Annotate Variants template workflow is a Genome Browser View linked with the variant table view.
You may be met with a warning as shown in figure 19.7. This is simply a warning telling you that it may take some time to create the table if you are working with tracks containing large amounts of annotations. Please note that in case none of the variants are present in ClinVar or dbSNP Common, the corresponding annotation column headers are missing from the result.
Figure 19.7: Warning that appears when you work with tracks containing many annotations.
Adding information from other sources may help you identify interesting candidate variants for further research. E.g. common genetic variants (present in the HapMap database) or variants known to play a role in drug response or other relevant phenotypes (present in the ClinVar database) can easily be identified. Further, variants not found in the ClinVar database, can be prioritized based on amino acid changes in case the variant causes changes on the amino acid level.
A high conservation level between different vertebrates or mammals, in the region containing the variant, can also be used to give a hint about whether a given variant is found in a region with an important functional role. If you would like to use the conservation scores to identify interesting variants, we recommend that variants with a conservation score of more than 0.9 (PhastCons score) is prioritized over variants with lower conservation scores.
It is possible to filter variants based on their annotations. This type of filtering can be facilitated using the table filter found at the top part of the table. If you are performing multiple experiments where you would like to use the exact same filter criteria, you can include in a workflow the Filter on Custom Criteria tool configured with the desired set of criteria.