The VEPFilter enables the filtering of VCF files annotated by VEP. The output is a VCF file containing the variants that have passed the filters.


Filter by Consequence
Here, you can select Sequence Ontology (SO) terms to filter variants according to their predicted consequences. The shown SO terms are ranked by their impact, from HIGH to MODIFIER. The VEP documentation gives detailed descriptions for each SO term. Press the Ctrl or Shift key to select multiple consequences. If you don't want to filter by consequences, select 'NONE'.
Choose LOF terms
This button allows you to easily select all SO terms that define loss-of-function (LOF) variants.
Further filtering conditions
Further filters can be specified as a comma-separated list of filter strings. Variants have to pass ALL filter strings. If variants should pass if they meet one of multiple conditions, use "or" in your filter string. For more information, see the documentation of the filtering script.
Folder for output files
Set the path to the folder where the filtered VCF file will be stored.
If "Overwrite" is checked, existing files will be overwritten.

Preference page

Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to
Set the path to the script used to filter VEP annotations. It can be found in the VEP installation in the ensembl-tools-release../scripts/variant_effect_predictor folder.

Input Ports

Cell 0: Path to VCF file.

Output Ports

Cell 0: Path to filtered VCF file.

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