If you are analyzing a list of variants, you can use the Filter Causal Variants (TAS-HD) ready-to-use workflow to remove variants that are outside the target region, as well as common variants present in publicly available databases. The workflow will annotate the remaining variants with gene names, conservation scores, and information from relevant databases.
To run the Filter Causal Variants (TAS-HD)) workflow, go to:
Toolbox | Ready-to-Use Workflows | Targeted Amplicon Sequencing () | Hereditary Disease () | Filter Causal Variants (TAS-HD) ()
- Double-click on the workflow name to start the analysis. If you are connected to a server, you will first be asked where you would like to run the analysis.
- Select the variant track you want to use for filtering causal variants (figure 22.44).
- In the next dialog, you have to select which data set should be used to filter causal variants (figure 22.45).
- Specify which of the 1000 Genomes populations that should be used for annotation (figure 22.46).
- In the next dialog, specify the 1000 Genomes population that should be used for filtering out variants found in the 1000 Genomes project.
- Specify the Hapmap populations that should be used for filtering out variants found in Hapmap (figure 22.47).
- In the last wizard step you can check the selected settings by clicking on the button labeled Preview All Parameters.
In the Preview All Parameters wizard you can only check the settings, and if you wish to make changes you have to use the Previous button from the wizard to edit parameters in the relevant windows.
- Choose to Save your results and click on the button labeled Finish.
The following outputs are generated:
- Amino Acids Changes Track that 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.
- Somatic Candidate Variants Track that holds the variant data. This track is also included in the Track List. 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.
- Track List 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 22.19).