Phenotype and covariate files should be in PLINK format. The first two columns should provide sample IDs, with subsequent columns providing values for each phenotype or covariate. The files can contain a header row, but then the first two elements must be either FID and IID or ID1 and ID2 (this option is new to LDAK 4.9). When a phenotype file contains more than one phenotype (i.e., more than three columns, you should specify which to analyse using the option –mpheno (regardless of whether you have column names). There is no option to select covariates (all covariates will be used).
Missing values should be denoted by NA. However, if a phenotype takes only values 0, 1 or 2, then LDAK assumes 1 corresponds to control, 2 to case and 0 denotes missing. Note that, whereas PLINK also treats -9 as missing, this is not the case in LDAK. When a phenotypic values is NA for a particular individual, then that individual is excluded from the analysis; however, if a covariate is NA, its value is replaced by the mean.