Add Information from Allele Frequency Community

The Add Information from Allele Frequency Community tool allows you to add AFC Frequency annotations from the Allele Frequency Community to variant tracks. 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 | Add Information from Allele Frequency Community

If you are connected to a server, you will first be asked 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 Add Information from Allele Frequency Community tool accepts a single variant track (Image variant_track_16_n_p) as input (figure 6.1).

Image afcannotate_input_selection
Figure 6.1: Select the variant track that you would like to analyze.

In the next dialog, you can specify your Ingenuity username, password and the reference sequence (figure 6.2).

Image afcannotate_account_info_step
Figure 6.2: Specify analysis parameters.

Finally, you can choose your 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 ethnic group specific frequencies (in percent) of the variants in the Allele Frequency Community. If the "AFC Frequency" column is empty for a variant, it indicates that the variant was not found in the Allele Frequency Community.