Remove Variants Found in Allele Frequency Community
The Remove Variants found in Allele Frequency Community tool allows you to add AFC Frequency annotations from the Allele Frequency Community to variant tracks, and to filter the variants based on those annotations. To be able to obtain AFC Frequency annotations from the Allele Frequency Community, your Ingenuity user account must be opted in to the Allele Frequency Community. The Changing Allele Frequency Community opt-in settings describes how to change your Allele Frequency Community opt-in status.
To start the tool, go to:
Ingenuity Variant Analysis | Remove Variants Found in Allele Frequency Community
If you are connected to a server, you will first be asked about where you would like to run the analysis. If you are not connected to a server, the first step is to specify the input for the analysis. The Remove Variants found in Allele Frequency Community tool accepts a single variant track (
) as input as shown in figure 7.1.
Figure 7.1: Select a variant track.
In the following wizard, specify your Ingenuity username, password and the reference sequence as described below (figure 7.2).
Figure 7.2: Specify analysis parameters.
- Ingenuity username: email address used to log in to Ingenuity Variant Analysis.
- Ingenuity password: password corresponding to your Ingenuity username
- Reference: Select the human reference sequence that is found under CLC_References in the Navigation Area. Complete human genomes (e.g., hg19 (GRCh37) and hg38 (GRCh38)) and subsets of these (e.g. individual chromosomes) can be used as references.
Click Next to go to the next wizard step. Here you can specify the cutoff for filtering by entering the desired value in the Maximum frequency field (figure 7.3). Only variants whose Allele Frequency Community frequency is equal to or lower than the specified value will be considered.
Figure 7.3: Specify the filter cutofff.
Click Next to go to the final wizard step where you can set the output options.
If you choose to open the results the two generated outputs will be opened in the View Area without being saved. In this case you will have to manually save the outputs if you would like to keep them. If you choose to save the outputs, they will not be opened automatically but will be saved at the destination you have specified.
When the analysis is finished, the resulting track will contain an additional column named "AFC Frequency", containing the observed frequencies (in percent) of the variants in the Allele Frequency Community. Furthermore, the number of variants will have been reduced according to the cutoff parameter that you have specified.
Note that if the "AFC Frequency" column is empty for a variant, it indicates that the variant was not found in the Allele Frequency Community. This can happen when the variant is a "new" one in the Allele Frequency Community database, but also for reference allele from an heterozygous pair whose non-reference allele was kept by the Remove Variants found in Allele Frequency Community tool as no reference variants are ever found in the Allele Frequency Community database. To filter out reference alleles, click on the "Filter" button in the variant table, select "Reference allele" in the drop-down menu, and keep only the alleles that contain "No". After this step, the only variants without an annotation in the "Community frequency" column will be the ones considered as "new" variants, i.e., not previously found in the Allele Frequency Community database.