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Difference between Genotype GVCFs and CombineGVCFs


I would like to be sure of the difference between those 2 tools.
From what I understand, GenotypeGVCFs somehow re-calculate likelihood and parameters (QUAL, DP, MQ...) for each variant positions present in at least 1 input sample. Right ? And is it not the case for CombineGVCFs?

Thank you for your help,

Best Answer


  • phhphh Member

    Will the output be different if I use GenotypeGVCFs without CombineGVCFs since GenotypeGVCFs can take multiple input? Thanks.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @phh

    In GATK4, the GenotypeGVCFs tool can only take a single input, so if you have GVCFs from multiple samples (which is usually the case) you will need to combine them before feeding them to GenotypeGVCFs. Although there are several tools in the GATK and Picard toolkits that provide some type of VCF or GVCF merging functionality, for this use case only two of them can do the GVCF consolidation step correctly: GenomicsDBImport and CombineGVCFs.

    Please let me know if this helps and if you need more information.


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