Filtering Logic
BaseSpace Variant Interpreter applies two levels of filtering. The first level is the base filter, which filters data by general information about the variants and is applied to all variants in the view. The second level applies more specific filtering criteria and is applied independently of other second-level filters.
Use the Exclude selector for a given filter to exclude matching variants. The default filter behavior is to include variants.
Filtering Example
In this example, the base filter captures small variants or copy number variants from a specific set of genes, where the variants pass filter and have an inheritance mode of de novo or recessive.
Secondary filter groups apply additional filters to the variants captured by the base filter. Two filter groups capture rare small variants and rare CNVs, using different thresholds for each. The CNV group includes additional criteria to exclude variants in regions that are challenging to call, thus removing potential false calls. A third filter group captures pathogenic CNVs and small variants regardless of their allele frequency.
Example Filter Configuration
