does GATK offers to match alleles in two vcf files?

[RezwanCAAS]

Hi GATK, I have done the steps, i.e., 1)haplotypecaller 2)combineGVCF 3) GenotypeGVCF. Now I am interested in performing the allele matching between two samples, like whether the alleles are the same or different at a particular chromosomal location. Does GATK offer to perform this test? if yes, then which function in GATK will be preferable?