Phenotypes and Covariates

Phenotype file format

Phenotypes are expected to follow the PLINK2 .pheno file format. This is a tab-separated format where the first column corresponds to the sample ID, and subsequent columns contain each of your phenotypes.

The first line of the file corresponds with the header and must begin with #IID. The names of each of your phenotypes belong in the subsequent columns of the header.

See tests/data/simple.pheno for an example of a phenotype file:

#IID    height  bmi
HG00096 1       3
HG00097 1       6
HG00099 2       8
HG00100 2       1
HG00101 0       4

Covariate file format

Covariates follow the same format as phenotypes.

See tests/data/simple.covar for an example of a covariate file:

#IID    sex     age
HG00096 0       4
HG00097 1       20
HG00099 1       33
HG00100 0       15
HG00101 0       78