Variant association analysis with both related and unrelated individuals

Question

[seta]

Dear all,

I'm going to do an association analysis of a set of common SNPs with some binary and quantitative traits, encompassing both related and unrelated individuals. As far as I know the package such as plink considered just unrelated samples, so it isn't appropriate for my case. Could you please let me know which package/tool you use in this situation?

Thanks

Answer 1

[Lemire]

You can use GEMMA, which implements linear mixed models to correct for structures in your sample (relatedness and population stratification).

https://github.com/genetics-statistics/GEMMA/blob/master/README.md

In addition, I believe GCTA can do the same thing:

https://cnsgenomics.com/software/gcta/#Overview

[seta]

Thank you very much.