Dear Pasi,
Thank you for sharing your knowledge. I'm just starting to use Lepmap3.
My goal is to create a genetic map from an F1 (fullsib population). I have some doubts about how to do it. I already have my VCF file, but not the pedigree.
I understand that I should create separate maps for each parent (mother and father), and then combine them with the offspring's map. How can I do this with LepMap3?
Sorry if my question is very basic, I'm a beginner!
Thank you very much!
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Normally you just construct one map, it will have male and female position for each marker. You can construct separate male and female maps as well, but you should first try with all markers.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Pasi,
Thank you for sharing your knowledge. I'm just starting to use Lepmap3.
My goal is to create a genetic map from an F1 (fullsib population). I have some doubts about how to do it. I already have my VCF file, but not the pedigree.
I understand that I should create separate maps for each parent (mother and father), and then combine them with the offspring's map. How can I do this with LepMap3?
Sorry if my question is very basic, I'm a beginner!
Thank you very much!
Dear Yess Alvarez,
Normally you just construct one map, it will have male and female position for each marker. You can construct separate male and female maps as well, but you should first try with all markers.
Cheers,
Pasi