Correction for among sample/chromosomes for sequenicng depth, when comparing between samples or animals

Question

[mohsamir2016]

Sorry for naive question. I am comparing between 5 animals regarding SNPs, and have counts for each chromosomes that I annotated using GATK (The Genome Analysis Toolkit (GATK) v4.3.0.0). I have also the genotypes being annotated. Now I am afraid that comparing number of SNPs across samples or animals or chromosomes, could be biased by the differences in sequencing depth between these. Is GATK pipleine corrects for sequenicng depth for instance within one VCF file between various chromosomes that might have various depth. If not how can I retrieve these information to plot depth vs n of SNPs per each chromosome ?

Thanks