Output from the Filter Somatic Variants (WGS) workflow

Two types of output are generated:

  1. Somatic Candidate Variants Track that holds the variant data. This track is also included in the Genome Browser View. If you hold down the Ctrl key (Cmd on Mac) while clicking on the table icon in the lower left side of the View Area, you can open the table view in split view. The table and the variant track are linked together, and when you click on a row in the table, the track view will automatically bring this position into focus.
  2. Genome Browser View Filter Somatic Variants A collection of tracks presented together. Shows the somatic candidate variants together with the human reference sequence, genes, transcripts, coding regions, and variants detected in ClinVar, 1000 Genomes, and the PhastCons conservation scores (see figure 15.18).

Image filter_somatic_variants_genome_browser_view1_wgs
Figure 15.18: The Genome Browser View showing the annotated somatic variants together with a range of other tracks.

The track with the conservation scores allows you to see the level of nucleotide conservation (from a multiple alignment with many vertebrates) in the region around each variant. Mapped sequencing reads as well as other tracks can be easily added to the Genome Browser View.

If you click on the annotated variant track in the Genome Browser View, a table will be shown that includes all variants and the added information/annotations. This is shown in figure 15.19.

Image filter_somatic_variants_genome_browser_view2_wgs
Figure 15.19: The Genome Browser View showing the annotated somatic variants together with a range of other tracks.

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 databases, 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 create a filter that can be saved and reused. To do this:

        Toolbox | Identify Candidate Variants (Image identify_candidate_variants_closed_16_n_p) | Create Filter Criteria (Image create_filter_criteria_16_h_p)

This tool can be used to specify the filter and the Annotate Variants workflow should be extended by the Identify Candidate Tool (configured with the Filter Criterion).

Note! Sometimes the databases (e.g. dbSNP) are updated with a newer version, or maybe you have your own version of the database. In such cases you may wish to change one of the used databases. This can be done with "Data Management" function, which is described in Download and configure reference data.