Estimating Variance Explained By Snps

Question

[Purpleone]

What is a standard approach to estimating the (phenotypic) variance explained by SNPs in a case/control GWAS?

I know about GCTA, but it's very computationally intensive. Are there simpler methods?

Answer 1

[Philipp Bayer]

You can do regressions in PLINK: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml

I did a small GWAS recently using a logistic regression for a binary phenotype in roughly 300 subjects and that took 2 seconds.

[kumar.vinod81]

Do plink also feasible for plant quantitative traits or it works only for binary phenotypes. I've tried with PLINK but at last in a unsuccessful manner. I want to try with it to confirm my GAPIT results but not finding a good way to analysis. Thanks