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CombineVCFs

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

Analogous to the CombineGVCFs the CombineVCFs can be used to merge VCF files of different samples into a single VCF. The resulting VCF file can then be further processed by filtering nodes. It is expected that the input is a list of two or more VCF files.
For further information, see GATK documentation of CombineVariants

Options

GenotypeMergeType

Desire how the genotype records for the samples should be merged.

UNSORTED: Take the genotypes in any order.
UNIQUIFY: Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
REQUIRE_UNIQUE: Require that all samples/genotypes be unique between all inputs.

Folder for output files

Set the path to the folder where the combined vcf file should be stored.

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 CombineVCFs.

Preference page

HTE: Set a threshold for repeated execution. Only used if HTE is enabled in the preference page. This will be done automatically if the path is already defined 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

: VCF files in the first column

Output Ports

: Merged VCF in the first column

Views

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

Best Friends (Incoming)

Column Rename (50 %) Streamable
String Input (50 %)

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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