Pileup mappability #19
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The previous mappability filter was a bit rough in how it addressed mappability, as it only really addressed if a read could uniquely map when starting at a given position. This doesn't really tell about how all the potential reads that can cross a position can map to it. Now the filter uses pileup mappability (see reference below), which averages the mappability of all possible k-mers overlapping a position. This should be more appropriate for telling how well a position can be mapped to with short read data. Setting K to a value close to historical DNA fragment sizes will hopefully make sure that modern and historical samples are getting fairly compared.
Fast Computation and Applications of Genome Mappability - Scientific Figure on ResearchGate. Available from: https://www.researchgate.net/figure/Pileup-mappability-The-number-of-all-possible-k-mers-covering-a-particular-position-of_fig4_221776385 [accessed 8 Dec, 2023]