chenli

Dear Pasi, I have an population with fourparents. You can see the cross design in the attachment cross.png. Is it right for me to use the pedgriee file in the attachment pedgriee.png ? P1 P2 P3 P4 and F7 indivaduals have been sequenced. Can lepmap3 handle this population？ If I use OrderMarkers2 grandparentPhase=1，the output of phased data is recording to which parent pairs ？ Pt1 and Pt2？ All the best, chenli

Dear Pasi, However, I use the normal pipeline and get the geneticmap, but when I run OrderMarkers2 grandparentPhase=1, I recieved error. I think this is reasonable because my population did not have grandparents. I shouldn't use the phased data of OrderMarkers2 for later QTL analysis. So I think I can use the genotpye data of the marker in the geneticmap, am I right? Thank you .

Dear Pasi, Thanks for the explanation. I did not use the Filtering2 in Lepmap3 , for you have said Filtering2 is more suitable for F2 population. I filtered the markers first before use Lepmap3. I am sorry for my poor english comprehension ability. I still want to confirm , is it right for me to follow the normal pipeline for my population ?

Dear Pasi, I have read the topic you write: https://sourceforge.net/p/lep-map3/discussion/general/thread/72ab43ec46/ I am confuse about the description you written in the topic. I have an RIL population of 216 individuals with unknown grandparents and parents. And I made a pedigree file like this： CHR POS F7 F7 F7 F7 F7 F7 ... CHR POS P1 P2 PP1 PP2 99 98 ... CHR POS 0 0 P1 P1 PP1 PP1 ... CHR POS 0 0 P2 P2 PP2 PP2 ... CHR POS 1 2 1 2 0 0 ... CHR POS 0 0 0 0 0 0 ... In this pedigree, P1 P2 are grandparents;...

Dear Pasi, I have read the topic you write: https://sourceforge.net/p/lep-map3/discussion/general/thread/72ab43ec46/ I am confuse about the description you written in the topic. I have an RIL population of 216 individuals with unknown grandparents and parents. And I made a pedigree file like this： CHR POS F7 F7 F7 F7 F7 F7 ... CHR POS P1 P2 PP1 PP2 99 98 ... CHR POS 0 0 P1 P1 PP1 PP1 ... CHR POS 0 0 P2 P2 PP2 PP2 ... CHR POS 1 2 1 2 0 0 ... CHR POS 0 0 0 0 0 0 ... In this pedigree, P1 P2 are grandparents;...