I am using Merlin to perform linkage analyses. I get the warnings "SKIPPED: Requires impossible recombination pattern". In Merlin's FAQs it is described that this is due to two markers have the same genetic position, but became recombined (=impossible). Indeed, I have about 5 % of markers in my dataset which share their genetic position with another marker (since I have NGS data there are often two SNVs only 3 or 4 bp apart from each other and those have the same genetic position).
Merlin suggests to "edit the map file to ensure that every marker maps to a unique position". Does anyone have an idea how to change the genetic position of duplicates like e.g. every second marker (of those with the same genetic position) is set 0.00001 cM further up? And most important: does this alteration influence my analysis? Or should I better remove every second marker with an equal genetic position (How to do so?)? BTW, I do not want to perform LD pruning.
Thanks in advance!