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CombineGVCFs

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

CombineGVCFs is meant to be used for hierarchical merging of gVCFs that will eventually be input into GenotypeGVCFs. One would use this tool when needing to genotype a too large number of individual gVCFs; instead of passing them all in to GenotypeGVCFs, one would first use CombineGVCFs on smaller batches of samples and then pass these combined gVCFs to GenotypeGVCFs. Note that this tool cannot work with just any gVCF files - they must have been produced with the Haplotype Caller as part of the "single sample discovery" pipeline using the '-ERC GVCF' mode, which uses a sophisticated reference model to produce accurate genotype likelihoods for every position in the target.
For further information, see GATK documentation of CombineGVCFs.

Options

Folder for output files
Set the path to the directory where the combined gvcf 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 CombineGVCFs.

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 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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GVCF files in the first column

Output Ports

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Merged gVCF 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)

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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