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.
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