How to set effect type of variants in a scoring file

Some polygenic scores may specify an effect type for each variant, for example PGS000802. Effect weights can be dominant, recessive, or additive (the default i.e., not dominant or recessive). Setting recessive or dominant effects will change allelic dosages when calculating a score.

Scorefile structure with effect types

Two additional columns are required to specify the effect type of each variant:

Optional effect type columns

is_dominant	is_recessive
TRUE	FALSE

These optional columns must be present after the four mandatory columns described in 2. Scorefile setup. These optional columns follow the structure described in the PGS Catalog scoring file format v2.0 and should be included after the effect_weight column.

Three possible effect types can be represented for each variant:

• Additive: both columns are FALSE

• Recessive: is_recessive is TRUE and is_dominant is FALSE

• Dominant: is_dominant is TRUE and is_recessive is FALSE

Note

The is_dominant and is_recessive columns are mutually exclusive (a variant cannot have a dominant and recessive effect type).

A scoring file with multiple effect types cannot contain multiple scores as described in How to apply multiple scores in parallel. However, using star (*) characters to match multiple scoring files will still work.