The segregating variants analysis falls in the category of algorithmic filters that can be performed on Family trio analyses.
It is a parameterizable algorithmic filter with the following options:
Segregating dominant variants
Variants annotated as pathogenic, likely pathogenic, or of unknown function (but only if one of the strong pathogenic Germine Variant Classification rules has fired for this variant) that are present (in any zygosity) in all affected samples and absent from all healthy samples. Select the "Strong VUS" option.
When selected, "Strong VUS" will keep variants of unknown significance (VUS) only if one of the strong pathogenic ACMG rules has fired for this variant. If not selected, any VUS that meets the filter's other criteria will be kept (irrespective of ACMG rules).
Strong rules are PVS1, PS1, PS2, PS3, PS4 and PP5. In addition, any rule whose strength has been raised to "strong", "very strong" or "stand alone" will be considered a "strong" rule, even if its original strength as per the ACMG guidelines was lower. For example, PM1 can be raised from "supporting" to "strong" if the variant is located in a dense hot-spot.
Segregating recessive variants
Variants annotated as pathogenic, likely pathogenic, or of unknown function (but only if one of the strong pathogenic Germine Variant Classification rules has fired for this variant) that are homozygous in all affected samples but heterozygous or absent from all healthy samples. Select the "Segregating recessive" option.
Compound heterozygous segregating
Variants present (in any zygosity) in all affected samples and absent from all healthy samples and it will also find possible segregating compound heterozygous variants: those variants annotated as pathogenic, likely pathogenic, or of unknown function that are found in genes where all affected samples have at least two so annotated heterozygous variants. Select the "Compound heterozygous segregating" option.
This option cannot be used in combination with the Segregating recessive option.
Running the analysis with multiple affected samples
Please note that this filter is not specifically designed for family trios, but for general multi-sample (e.g. cohort) analyses. When running it with multiple affected samples, it will look for variants that are homozygous in all affected samples and absent or heterozygous in all healthy samples. The segregating variants (dominant) filter will look for variants that are present (het or hom) in all affected samples and absent in all healthy samples.