There are a number of mappability tracks in the UCSC browser many of which have different/similar k-mer versions. I choose the ones that are similar to the k-mer lengths we use in our mapping process but my question is: What are the main issues when deciding which one of these tracks to use? Are they simply interchangeable if they have the same k-mer option? What is your heuristic to choose from among those tracks when you use them?
I would like to see if there is a relationship between the mappability of a region (as defined by the track) and the genotypes I detect using exome sequencing (illumina)