calls for single cell sites without any coverage

[dlaehnemann]

@aschoen, @alicemchardy and I just discussed this possible future idea to extend the statistical model for sites where there is no coverage in a particular cell, but possibly in the respective bulk sample. In this case, another of coverage vs. no-coverage would have to be added, where the coverage part is covered by the existing model and the no-coverage part would have to be newly defined. The major challenge is, that the beta-binomials of the empirical model are not defined for a coverage of zero, so instead something like a general or cell-specific heterozygosity prior would need to be used. In combination with the bulk likelihoods, this might still give reasonable likelihoods, although the comparability with the existing model would need to be looked at in detail before e.g. trying a joint false discovery rate control on sites with and without coverage in a particular single cell.

[johanneskoester]

In such a case, likelihoods should be all 1 for the SCS. Then, if a heterozygosity based prior is used, posteriors will naturally adjust to the best guess based on the bulk data alone.