1) If the sex of offsprings in a family is not available can I set it to 0 in the ped file , while I set FATHER to 1 and MOTHER to 2
2) Is there a way to visualize ordered markers into graphical format like genetic map of LGs seen in publications. I understand we can convert ordered markers of a given chromsome into dot file but that doesnt appear like standard LG image.
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Two more questions:
3) If we have PL or GL field in VCF file, would it be automatically included in the analysis by LM3 or we must make a separate ped file with PL info ?
4) how to make a ped file with posteriors (from PL) for LM3. Right now my ped file does not contain posterior info.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear All,
1) If the sex of offsprings in a family is not available can I set it to 0 in the ped file , while I set FATHER to 1 and MOTHER to 2
2) Is there a way to visualize ordered markers into graphical format like genetic map of LGs seen in publications. I understand we can convert ordered markers of a given chromsome into dot file but that doesnt appear like standard LG image.
Two more questions:
3) If we have PL or GL field in VCF file, would it be automatically included in the analysis by LM3 or we must make a separate ped file with PL info ?
4) how to make a ped file with posteriors (from PL) for LM3. Right now my ped file does not contain posterior info.
Dear krishna,
I am creating a new thread for this in LM3 forum. https://sourceforge.net/p/lep-map3/discussion/general/thread/11f56293/#627d
Cheers,
Pasi
Last edit: Pasi Rastas 2018-03-22