GenotypeGVCFs merges gVCF records that were produced by the HaplotypeCaller, or result from combining such gVCF files using CombineGVCFs. This tool performs the multi-sample joint aggregation step and merges the records together in a sophisticated manner: at each position of the input gVCFs, this tool will combine all spanning records, produce correct genotype likelihoods, re-genotype the newly merged record, and then re-annotate it.
For further information, see GATK documentation of GenotypeGVCFs.


Number of threads
Set the number of threads to be used. Increasing the number of threads speeds up the node, but also increases the memory required for the calculations.
Folder for output files
Set the path to the folder where the output files should be stored.


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 GenotypeGVCFs.

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

Input gVCF file

Output Ports

Genotyped VCF


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




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