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VCFMerger

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

The VCFMerger is based on the GATK CombineVariants. It reads in multiple variant records from separate ROD (Reference-Ordered Data) sources and combines these variant records present at the same site in the different input sources into a single VCF. Any number of sources can be input.
For further information, see the GATK documentation.

Options

CombineVariants options

Add VCF files
This option enables to either add one single input VCF file by setting its path or several VCF files, which are located in the same folder and match the given regular expression (regex). In the latter case you have to set the path to the folder.
Currently selected VCF files
Selected VCF files are listed in the box and will to be merged. This option allows you to remove undesired files.
Genotype Merge Type
Determine how genotype records for samples shared across the ROD file should be merged.
  • UNSORTED: Take the genotypes in any order.
  • UNIQUIFY: If sample names overlap, then they are "uniquified", which means a suffix is appended to make them unique. Each sample shared across RODs gets named sample.ROD.
  • REQUIRE_UNIQUE: Require that all samples/genotypes be unique between all inputs.

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 VCFMerger.

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.

Output Ports

Icon
Path to the merged VCF file

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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