• The new make_vcf_format() function within the polyrad2vcf is different than how it is implemented in dosage2vcf and updog2vcf. This is much faster than the previous formats, and does not rely on reshape2.
  • Check that those other versions correctly concatenate the FORMAT information from the different dataframes

Regarding the error when getting dosage_ratios() for the boxplot, I am not sure why that happens in the Genotype Diversity tab. I was not able to identify any obvious formatting errors here that were different than previous VCF formats and could be impacting how the dosage calls are viewed. Note: All of the modules rely on converting the GT field to discrete dosage calls, so the issue could be in how that field is formatted, not the UD field.

• I removed the ability to select for the _LD options for now until we do more testing and allow for users to select more custom options

I could not get the download button to be disabled (or not be present ), until the analysis completes. WIll need to update the UI if not already adjusted in other pull requests.

Added support for svg(), and will need to extend this to all image downloading functions

For Updog, the dosage calls are usually based on the count of reference alleles, where 0 = homozygous alternate. I am assuming that DArT using the standard Updog parameters, so it is likely also that count