When I recently ran RepairPal through the paces with a real list of repairs (Front pads, front rotors, bracket sensor, air filter, spark plugs, fuel filter, marker filter, and oil service) it came up with estimates for all but two items for my model vehicle.
For example, the Marker filter in Ensembl's MartView has two parameters, start and stop.
(Note that such marker filtering also effectively eliminates any sequencing and PCR error from the data).
Predictive ability of each marker filtering criteria was evaluated using 10-fold cross validation replicated 200 times.
This approach, however, requires tightly physically linked markers data and substantial population differentiation (otherwise the correlation in FST between linked will remain poor even with stringent marker filtering).
However, due to the effects of random sampling, sequencing errors misalignments, and residual parental allele bias that may remain after marker filtering, the distribution is skewed.
Overall, marker filtering criteria did not have a large effect on for GY, but some important effects were observed for PH and MD.
For 12 Mb of the chromosome we generated random subsets of the full datasets with varying sample size, and then performed marker filtering and map generation as described.
Only three studies report marker filtering according to some minor allele frequency threshold ([ 18, 26, 27]; the latter study excluded singleton loci only, i.e., markers with the minor allele occurring only a single time).
We used strict marker filtering, followed by an HMM where transition and emission probabilities were estimated sample-wise using a beta-mixture model on the estimated parental allele frequencies within sliding windows.
We suggest that a reasonable strategy to define and eliminate uninformative polymorphisms should be chosen by inspecting the allele frequency distribution of the polymorphisms, and by assessing the influence of different marker filtering thresholds on the genomic patterns of interest, or appropriate statistics (such as the correlation of FST between sister RAD sites).
