I remembered why the VCF filtering plots do not populate until the user selects "Apply Filters" - This is because Updog will impute all sites, so the SNP and Sample histograms will appear as 0 missing data until the user selects the min read depth value to convert dosage calls to NA. To get around this, I am using the read depth value provided by the user, and displaying both pre- and post- filtered VCF plots after applying the filters.