The Fixed Ploidy Variant Detection tool has two parameters. The ploidy level you set defines the statistical model that will be used during the variant detection analysis and thereby also defines what will be reported. The number of alleles that variant may have depends on the value that has been chosen for the ploidy parameter. For example, if you chose a ploidy of 2, then the variant at a site could be a homozygote (two alleles the same in the sample, but different to the reference), or a heterozygote (two alleles different than each other in the sample, with at least one of them different from the reference). If you had chosen a ploidy of three, then the variant at a site could be a homozygote (three alleles the same in the sample, but different to the reference), or a heterozygote (three alleles different than each other in the sample, with at least one of them different from the reference).
The variant probability parameter defines how good the evidence has to be at a particular site for the tool to report a variant at that location. If the site passes this threshold, then the variant with the highest probability at that site will be reported.
Sensitivity of the tool can be altered by changing these parameters: to increase sensitivity, you could decrease the variant probability setting - more sites are being reported - or increase the ploidy - adding extra allele types.
For example, a sample with a ploidy of 2 has many C and a few G at a particular location where the reference is a T. There is high enough evidence that the actual position is different than the reference, so the variant with the highest probability at this location will be reported. In the diploid model, all the possibilities will have been tested (e.g. A|A, A|C....C|C, C|G. C|T....and so on). In this example, C|C had the highest probability, and as long as the relative prevalence of Gs is low compared to Cs - that is, the probability of C|C stays higher than C|G - C|C will be reported. But in a case where the sample has a ploidy of 3, the model will test all the triploid possibilities (e.g. A|A|A, A|A|C, A|A|G.....C|C|A, C|C|C, C|C|G.... and so on). For the same site, if the evidence in the reads results in the variant C|C|G having a higher probability than C|C|C, then it would be the variant reported. This shows that by increasing ploidy we have increased sensitivity of the tool, reporting a variant that represents the reads with G as well as the ones reporting a C at a particular position.