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.
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