- The statistical model. Here the ploidy you set is crucial to the model and what will be detected.
- The variant probability setting. This affects which locations will be reported.
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.