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Variant association analysis with both related and unrelated individuals

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

association analysis releatedness package/tool
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updated by Lemire Lemire • written by seta seta

1 answer

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

• 0 views • link
written by Lemire Lemire

Thank you very much.

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written by seta seta

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