Ploidy and sensitivity

Core to how this tool works is the ploidy level you set. This defines the statistical model that will be used during the variant detection analysis and thereby also defines what will be reported. When you set up a Fixed Ploidy Variant Detection, you provide a ploidy and you also provide a variant probability. 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, (note that it's 'the site' and not 'the variant' here), then the variant with the highest probability at that site will be reported. That is, at a given location, you get one variant 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). So how sensitive this tool is, in terms of what it detects and reports to you, will be down to:

So, to increase sensitivity, you could decrease the variant probability setting or increase the ploidy. The increased sensitivity due to decreasing the variant probability setting is due to more sites being reported on. This could decrease false negatives, but it could also increase your reporting of false positives.

The increased sensitivity you would get by increasing the ploidy level is down to the extra allele types that will be included in the model and thus reported to you in the results. For example, let's say you set a ploidy of 2 and at a particular location, where the evidence that the position was different than the reference was high enough, the reference was a T. The variant with the highest probability at this location will be reported. Let's say that it was a homozygote with C at that position. So that's C|C. However, let's say that in fact, there are some Gs reported at that site in some reads. 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). However, in this example, C|C had the highest probability, so it is reported. It doesn't really matter how much deeper the mapping is at that location if the relative prevalence of Gs is low compared to Cs. (That is, the probability of C|C will stay higher than C|G if there were relatively few Gs at this site, so C|C would be reported as long as this stayed the case.) Let's say that you chose a ploidy of 3 instead. Now 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). Now, for the same site, say that the evidence in the reads resulted in the variant C|C|G having a higher probability than C|C|C, then it would be the variant reported. So in this way, you have increased the sensitivity. i.e you have reported a variant that represents the evidence of the reads with G at that position as well as the ones reporting a C at that position.