0 ×

VEPFilter

IBIS Helmholtz-Node extension for KNIME Workbench version 1.8.1.201707071203 by IBIS KNIME Team

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.

Options

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

HTE
Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to filter_vep.pl
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

Icon
Cell 0: Path to VCF file.

Output Ports

Icon
Cell 0: Path to filtered VCF file.

Views

STDOUT / STDERR
The node offers a direct view of its standard out and the standard error of the tool.

Best Friends (Incoming)

  • VEP (100 %) 

Best Friends (Outgoing)

  • VEP (100 %) 

Installation

To use this node in KNIME, install KNIME4NGS from the following update site:

KNIME 4.3

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.