Imputing missing phenotypes

[zmy24]

Hi, I have a phenotype data with some missing value. And I found the Fastqtl will impute the issing phenotypes automatically. I wonder if it was imputed by the average value? And how can I avoid imputation?

[francois-a]

Yes, missing phenotypes are mean-imputed. To avoid this, you either need to filter out phenotypes with missing values, or impute them using an alternate method prior to running fastQTL.