Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics
Fig 2
The steps of Recombulator-X are represented on the left column of the figure, while we reported a simplified example on the right using just three X-STRs.
1) Preprocessing: Recombulator-X reads the PED file, performs preliminary quality checks, extracts the informative type I and type II families and phases all the females, whenever their father is available. 2) Likelihood computation, depending on the family type: in the case of a phased mother (type I family), the likelihood (L1) of each possible recombination is computed and summed up. Here, the red crosses indicate genetic incompatibilities (mutations greater than one repeat), while the single red lines correspond to compatible single-step mutations. When the grandfather is not available (and thus the mother cannot be phased, type II family), this process is repeated for each possible maternal phase (L2). 3) In the last step—optimization—the likelihood of the entire dataset is computed by multiplying together the likelihood of each family and Recombulator-X searches the parameters (recombination and mutation rates) that maximize the global likelihood.