Filtering Logic

Filtering Logic

Connected Insights applies two levels of filtering. The first level is the condition group, which filters data by general information about the variants and is applied to all variants in the view. The second level includes other condition groups with more specific filtering criteria that are applied independently from other condition groups of the second-level filters.

❗ If you are building a filter that covers multiple variant categories, make sure that second level filters cover each of the variant categories that you intend to return with the filter. Including a variant category in the first level filter (eg, copy number variants) but omitting it in second-level filters (even if without filtering conditions) excludes this variant category from the filtering results. For example, filtering logic (Small Variants, CNVs, SVs) AND((Small Variants) OR (CNVs)) excludes SVs from the filtering results. Refer to the following filter examples for more details.

Use the Exclude selector for a given filter to exclude matching variants. The default filter behavior is to include variants.

First-Level Condition Group

The first-level condition group:

• Does not specify any conditions for genes, thereby including into the filtering results variants from all genes.

• Includes into the filtering results all variant categories that Connected Insights supports (for example, small variants SVs, CNVs, RNAsplice variants, and RNA fusions variants).

• Sets a condition to include only variants that have PASS in the VCF variant filters, thus excluding all variants that do not have a PASSvalue.

The first-level condition group is connected to the second-level condition groups via operator AND.

Second-Level Condition Groups

The first of the second-level condition group specifies inclusion criteria for small variants to be returned in the filtering results. The condition group sets criteria to capture rare small variants with specific consequences that are of interest:

• Variant category is set to Small Variant

• Population frequency is specified as equal or less than 0.05 in five population groups in gnomAD

• The Consequences filter lists categories of interest: Start Loss, Stop Gained, Stop Loss, and others

The small variants condition group is connected to other second-level condition groups via the operator OR.

The third second-level condition group provides inclusion criteria for RNA Splice Variants. Only PASS-ing (per first-level condition group) RNA Splice Variants with consequence Exon Loss Variant are included in the filtering results.

The next second-level condition group provides inclusion criteria for RNA Fusion Variants. This filtering logic only includes PASS-ing (per first level condition group) Unidirectional Gene Fusions in the filtering results.

The last second-level condition group lists structural variants and copy number variants as variant categories but does not provide any filtering condition. In the current version of Connected Insights, such condition group is required to include structural variants and copy number variants in the filtering results even though they are already specified in the first-level filter.