合并不同样本的vcf用MergeVCFs ；合并不同染色体vcf可以用GatherVCFs/concat

First of all, there is no CombineVariants. I think you were going for CombineGVCFs. This program is used to combine GVCFs from different samples.

GATK offers two Picard tools for what you want and they have different prerequisites:

MergeVCFs merges complete (whole genome) VCF's from different individuals into one. <- I think this is the one you want.

GatherVCFs merges vcfs that contain all individuals but each contain a different part of the genome. (for example 1/3, 2/3 and 3/3 parts on genome into whole genome).

https://gatk.broadinstitute.org/hc/en-us/community/posts/360071192131-Merge-different-individual-VCF