Merlin file format, two markers have the same genetic position

Question

[stu111538]

Hi,

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!

[jojo]

Hi, I am having this same problem at the moment and I'm now looking for a script to add 0.00001cM onto duplicate values in my map files. How did you end up overcoming your problem? Did you happen to write a script that you could share? Kind regards.

Answer 1

[el.zablotskaya]

You can remove all the positional duplicates in your file if the total number of markers is big enough. If you don't want to loose any markers, change their genetic position, it's not likely to affect linkage results. If you don't feel confident to write a small script to do the job, you may try to do it in Excel (remove duplicates option, IF function...).

Note that Merlin can throw the same error message when there are other problems with your map file, for example, if you have commas as a decimal separator instead of dots.