analysis of gvcf file

Question

[wongzlll]

Hi, how can i analyze the vcf file after using HaplotypeCaller? What is the counting of SNPs for and how can i compare it with the assembly size?

[Kevin Blighe]

...what is the goal of your work? Please also inform of what assistance [locally] that you may have?

If you already used HaplotypeCaller, then I assume that you already have technical ability, and also an ability to follow documentation.