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VEP

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

This node is a wrapper for Ensembl's Variant Effect Predictor (VEP) which annotates genomic variants. The tool provides various annotation options and allows you to include individual plugins. The node supports the application of the LOFTEE plugin which assesses the confidence of loss-of-function variant.

Options

Annotation

Coding only
If this box is checked, VEP will only return consequences that affect coding regions of transcripts.
Choose transcript set
VEP uses Ensembl transcripts (=GENCODE Comprehensive) by default. By choosing GENCODE Basic your analysis is limited to transcripts without fragmented or problematic transcripts. Alternatively, you can choose the RefSeq transcript set (requires the RefSeq cache or not using the cache).
SIFT
Check this box, if you want VEP to output the prediction term and score of amino acid substitutions predicted by SIFT.
PolyPhen
Check this box, if you want VEP to output the prediction term and score of amino acid substitutions predicted by PolyPhen.
Gene symbol
VEP adds the gene symbol (where available) to the output.
Biotype
Adds the biotype of the transcript or regulatory feature.
Further flags
Commit further options to VEP (whitespace separated).

Performance

Number of forks
Enable forking, using the specified number of forks. Forking can dramatically improve the runtime of the script. If LOFTEE is used, it will run ignoring the conservation file as there occur errors when the file is accessed by multiple threads.
Buffer size
Sets the internal buffer size, corresponding to the number of variations that are read in to memory simultaneously. Set this lower to use less memory at the expense of longer run time, and higher to use more memory with a faster run time.
Use cache
It is recommended to use a cache as accessing data in the cache is much faster than accessing it from the database. The cache is usually build during the installation of the Ensembl API. Otherwise, you can find information in the VEP documentation (see VEP link above).
Cache directory
Set the path to the cache directory.
(Default: "$HOME/.vep/")
Path to FastA file
Specify a FastA file or a directory containing FastA files to use to look up reference sequence. The file is required for the flags --hgvs or --check_ref when the cache is used. Moreover, the plugin LOFTEE won't work properly if no FastA file is given! The FastA can be downladed using the VEP installation script. In general, it is located in the cache directory (which is shown as default).

Output

Choose format of annotation file
VEP outputs a tab separated file by default. It can also create a GVF or JSON file or add the annotations to the input VCF file.
Choose format of statistics file
VEP can create a statistics file in html or plain text format.
Folder for output files
Set the path to a folder where the output files should be stored.
If "Overwrite" is checked, existing files will be overwritten.

Plugins

Plugin directory
Set the path to the plugin directory.
(Default: "$HOME/.vep/Plugins")
Further plugins
Commit further plugins to VEP. If you want to use multiple plugins, separate each plugin by whitespace.

LOFTEE

Use LOFTEE
Check this box if you want to use LOFTEE. Requires the plugin file in the plugin directory.
Path to human_ancestor.fa.gz
You can find a download link for this file following the LOFTEE link above.
Path to phylocsf.sql
You can find a download link for this file following the LOFTEE link above. The conservation file will be ignored, if forking is enabled.

Preference page

HTE
Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to variant_effect_predictor.pl
Set the path to the VEP perl script. It can usually be found in ensembl-tools-release-../scripts/variant_effect_predictor.
Samtools PATH
Set the path to the SAMTOOLS executable (required by the LOFTEE plugin).

Input Ports

Icon
Cell 0: Path to VCF file.

Output Ports

Icon
Cell 0: Path to annotation file in the specified format.

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.3

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Developers

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