Population-level variant calling using accessions with complex ploidy level

[mirror110]

Hi,
I am going to carry out the variant calling using two hundreds accessions with low sequenging depth (majority of them around 2-5 x), but for each species, there are around 8 accessions with high sequencing depth (from 10-30 x). Meantime, all of these accessions also have complex ploidy level, ranging from diploid to hexaploid. Given the low sequencing depth, I wanna conduct the population-level variant calling, but I have no idea how I should deal with the following issues.

First, of these accessions, there are around 30 accessions with unkown ploidy level.
Second, how should I set the ploidy-level in the same run? Or, currently, it is impossible for me to conduct the population-level variant calling using all of these samples at once.

Thanks.

Sincerely.