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SnpEff

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

SnpEff annotates and predicts the effects of genetic variants.
Source: http://snpeff.sourceforge.net/SnpEff.html

Options

Database name
In order to produce the annotation, SnpEff requires a database.
For more information, see http://snpeff.sourceforge.net/SnpEff.html
Use database directory specified in config file?
Uncheck this option, if you want to use another database directory. If the chosen database is not available, it will be downloaded. Note, that downloading may take some time depending on the size of the database.
Path to BED file
Only analyze changes that intersect with the intervals specified in this BED file.
Java Memory
Set the maximum Java heap size in GB.
Further options
Set additional command line flags.

Results filter

Do not show ... changes
Choose regions in which variants will not be annotated.

Preference page

HTE
Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to snpEff.jar
Set the path to the snpEff jar file.

Input Ports

Icon
Input VCF file

Output Ports

Icon
Annotated VCF file

Views

STDOUT / STDERR
STDOUT / STDERR
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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