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GATKSelectVariants

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

This node is based on the SelectVariants tool of GATK. It can be used for selecting subsets of variants from a VCF containing many samples and/or variants.
For further information, see GATK documentation of SelectVariants.

Options

Select Variant Type
Select the variant type (SNP or indel) which should be in the resulting subset file.

GATK

GATK Memory
Set the maximum Java heap size (in GB).
Path to BED file
You can check this option to perform the analysis in certain genomic regions. You have to specify the intervals in a text file in BED format and select the file in the file browser.
Further options
Set additional command line flags for the GATKSelectVariants.

Preference page

HTE
Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to reference sequence
Set the path to the reference reference sequence. This will be done automatically if the path is already defined in the preference page.
Path to GATK jar file
Set the path to GenomeAnalysisTK.jar. This will be done automatically if the path is already defined in the preference page.

Input Ports

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Cell [1..x]: Path to VCF input file Exact column can be selected by using the node parameters

Output Ports

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Cell 0: Path to a subset VCF file containing SNPs or indels

Views

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

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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