(1) Convert your output to chi-squared values

(2) Calculate lambda gc (λgc)

If analysis results your data follows the normal chi-squared distribution, the expected λgc value is 1. If the λgc value is greater than 1, then this may be evidence for some systematic bias that needs to be corrected in your analysis.

(2) Calculate lambda gc (λgc)

If analysis results your data follows the normal chi-squared distribution, the expected λgc value is 1. If the λgc value is greater than 1, then this may be evidence for some systematic bias that needs to be corrected in your analysis.

How about for imputed data? Should we thin the markers to retain only SNPs with minimal-no LD first? Or the GIF from pre-imputed plink runs (with --adjust) can be used? Thank you.

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