Gene Category Type and Variant Effect filter types can be applied to the same variants

The Gene Category Type (GCT) has a functional type parameter similar to ‘Variant Effect’ which you can set when creating a custom trio analysis workflow. Both this functional type selection and Variant Effect will be applied if used together in a filter chain. For example, if a variant has a GCT functional type of INDEL, it may have a Variant Effect type of frameshift or non-frameshift. The functional annotation types differ for these two filter types.

The GCT functional filter types are as follows:

  • SNP


  • synonymous

  • missense

  • stoploss

  • stopgain

  • splicejunction

  • utr

The Variant Effect filter types are as follows:

  • unknown

  • synonymous

  • missense

  • nonframeshiftInsertion

  • nonframeshiftDeletion

  • nonframeshiftBlockSubstitution

  • nonsense

  • stoploss

  • frameshiftBlockSubstitution