Recoquillay Julien

Thanks Pasi. I did not see that you had answered. So basically, JoinSingle2All said this : If you asked for the high and technically allowing anything LOD of 30, SNP goes to Linkage Group 34. If asked for a lower LO of 4.4 -> LG 3 and a lower again LOD of 3.3 -> LG 4 Many thanks, I understand better the output now.

Hello Pasi, Not an issue this time as all is working fine. I juste have a question on JoinSinglesAll Output. What are the numbers after the linkage group ID for the marker integrated in a new linkage group as in this example : 34 0 34 23.811889455274443 3 4.410338025559511 4 3.3456959964294652 Are they LODscore ? Is the ordering indicative of what should be kept ? Best regards, Julien.

Thanks Pasi. Trying it right now. EDIT : Situation solved. Thanks Pasi. Until the next :D

Thanks Pasi. Trying it right now.

Of course, Here are attached the first 50 lines.

Hi Pasi, The Parenttest.txt comes from ParentCall2. I tried to rename it p.call as in your example in the wiki but it had not effect. Do you think that re-runing the ParentCall2 but with p.call as the output file will be better ? Thanks, Julien. EDIT : I re-launched the ParentCall2 analysis with this command : nohup java -cp /home/julien/lep-map3/bin ParentCall2 data=PedFormatLep3p.txt vcfFile=mapf2.vcf > p.call EDIT2 : Command after run of command in EDIT : java -cp /home/julien/lep-map3/bin Filtering2...

Hi Pasi, The Parenttest.txt comes from ParentCall2. I tried to rename it p.call as in your example in the wiki but it had not effect. Do you think that re-runing the ParentCall2 but with p.call as the output file will be better ? Thanks, Julien. EDIT : I re-launched the ParentCall2 analysis with this command : nohup java -cp /home/julien/lep-map3/bin ParentCall2 data=PedFormatLep3p.txt vcfFile=mapf2.vcf > p.call EDIT2 : Command java -cp /home/julien/lep-map3/bin Filtering2 data=p.call dataTolerance=0.001...

Hi Pasi, The Parenttest.txt comes from ParentCall2. I tried to rename it p.call as in your example in the wiki but it had not effect. Do you think that re-runing the ParentCall2 but with p.call as the output file will be better ? Thanks, Julien. EDIT : I re-launched the ParentCall2 analysis with this command : nohup java -cp /home/julien/lep-map3/bin ParentCall2 data=PedFormatLep3p.txt vcfFile=mapf2.vcf > p.call