Can't determine any relatedness using lcMLkin
Does anyone here use the software lcmlkin for relatedness estimation?
I am having some trouble and would like to ask some questions.
EDIT:
Basically, I can't determine any relatedness between individuals who I know are related. (the CEPH family)
I am using the CEU population in 1000G as a reference. I have tried thinning the snps by 10K, 100K, and 150K distance between. I have tried filtering by a MAF of 0.1 and 0.15
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Just ask your question and you will see if someone can help you. I would suggest you edit your post for this.
It would help if you posted the command you executed and the first lines of the output. Alternatively you can just mention what results you were expecting and what results you got. So, if some expert of the software is around can have a chance to understand what's going on.