Aggregate Filtered Variants

Note

This algorithm runs on the variants in the selected Filter Chain and not all variants originally imported.

Requirements

This algorithm requires first annotating and classifying variants using a gene annotation source.

After clicking OK you will be prompted to select a Gene Names field to group variant counts based on genes, and a grouping field. If no grouping is selected, counts will be created for all of the combined samples. Otherwise the values in the selected Category field which is used to define the sample sets.

Output in the Gene Table

Three different fields will be created for each sample set. A sample set is created for each category in the selected Category field, as well as for a ungrouped set which contains all of the samples. Each category will have the three following fields for each gene.

Fields include:

  • Unique Variant Count: The total number of unique variant sites that are present for this sample category.
  • Unique Sample Count: The total number of samples in this bucket which had variant sites in this gene.
  • Observed Variant Count: The total number of different variant sites observed in this gene across all samples.

Output in the Filter Chain

A filter card is automatically created after the algorithm finishes running. This card is placed at the bottom of the filter chain, but can be moved by clicking and dragging the card to the desired location.

If moving the algorithm output card changes the input it will be necessary to rerun the algorithm. This will be indicated by an information icon on the filter card.

By default the filter card created will correspond to the Unique Variant Count field, but can be changed to other fields created by the algorithm. Additionally, right-clicking on the column header for the other fields produced will present an option to add an additional card for that field.