Open huijie615 opened 1 month ago
Hi Huijie, thanks for the question, and sorry for the problems.
Yes, the problems occur when searching for individuals with both a phenotype and their mother in the data.
LDAK first seems which individuals have a maternal ID (ie, column 4 of the fam file is NOT "0") - let's denote these individuals List1 - there are 499
Then LDAK sees which List1 individuals have phenotypes - let's denote these individuals List2 - there are 475
Lastly, LDAK sees which List2 individuals have their mother in the data. This is where LDAK finds zero. Ie, while there are 475 individuals with phenotypes, and a maternal ID, LDAK is unable to find any of the mothers for these individuals in the data. If you look at the fam file, does that sound correct?
Then please check for small typos. E.g., suppose the first two rows of the fam file are Fam1 Ind1 0 Ind2 0 0 Fam1 Ind2 0 0 0 0 Then the individual "Fam1 Ind1" has a maternal ID, and their mother is called "Fam1 Ind2", who is IN the data
However, if the rows were Fam1 Ind1 0 ind2 0 0 Fam1 Ind2 0 0 0 0
or Fam1 Ind1 0 Fam1_Ind2 0 0 Fam1 Ind2 0 0 0 0
etc, then LDAK can not find the mother
Thanks
Hi Doug, I'm currently using LDAK (Version 6) for my analysis, and I've encountered an error that I'm struggling to resolve. Here are the details of the issue:
This error seems to arise during the "Find duos" process. It indicates that none of the 1108 individuals have phenotypes and their mother in the data. However, I do have 475 offspring with phenotypes and their mothers' IDs (as recorded in the log file), so I'm unsure why this error occurs.
Could you please provide any suggestions for resolving this issue?
Best regards, Huijie