Count Alleles By Gene


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


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.

Output in the Gene Table

The fields in the gene table include sample specific fields for three different categories. The counts in each field are based on the grouping of unique values from the selected Gene Names field from the specified annotation source.

Fields include:

  • # Variants: The total number of variants for the current sample in each gene.
  • Allele Count: The total number of non-reference alleles for the current sample in each gene.
  • # Het: The total number of heterozygous variants for the current sample in each gene.
  • # Hemi: The total number of hemizygous variants for the current sample in each gene.
  • # HomoVar: The total number of homozygous variants for the current sample in each gene.

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 # Variants field, but it 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.