Combines any number of gVCF files that were produced by the Haplotype Caller into a single joint gVCF file.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


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 too large a 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.


One or more Haplotype Caller gVCFs to combine.


A combined VCF.


 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T CombineGVCFs \
   --variant gvcf1.vcf \
   --variant gvcf2.vcf \
   -o mergeGvcf.vcf

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by CombineGVCFs.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Window size

This tool uses a sliding window on the reference.

  • Window start: 0 bp before the locus
  • Window stop: 1 bp after the locus

Command-line Arguments

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

CombineGVCFs specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Inputs
NA One or more input gVCF files
Optional Outputs
stdout File to which the combined gVCF should be written
Optional Flags
false If specified, convert banded gVCFs to all-sites gVCFs

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

--convertToBasePairResolution / -bpResolution

If specified, convert banded gVCFs to all-sites gVCFs

boolean  false

--out / -o

File to which the combined gVCF should be written

VariantContextWriter  stdout

--variant / -V

One or more input gVCF files
The gVCF files to merge together

R List[RodBindingCollection[VariantContext]]

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA