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.


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 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

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

This node has no input ports

Output Ports

Path to the merged VCF file

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