File formats

When possible, we try to use standard file formats for grstools. For instance, genotype data from various well-known file formats like VCF or plink are understood. Because we are not aware of standards for the description of genetic instruments, we define some expected file formats.

The GRS format

The GRS format is used to describe genetic variants with a known effect size. In grstools it is used for two things:

• To select variants from association summary statistics from large meta-analyses.
• To compute the GRS based on genotype data.

The GRS format is a comma-delimited file containing the following columns:

• name (mandatory unique identifier)
• chrom (e.g. “1”, “22”, “X”, “MT”)
• pos (the position e.g. 68184194)
• reference (the allele that is used as the reference in the effect estimate)
• risk (the risk, or effect allele)
• p-value (mandatory for the selection of variants but optional for the computation of the GRS. This is the association p-value)
• effect (a weighting term used in the computation of the GRS. Concretely, this is likely to be an estimated \(\beta\) or odds ratio).

Optional columns are also useful in some cases:

• maf The minor allele frequency can be used in the selection of variants or to optimize LD computations by removing rare variants. It can also be used to distinguish ambiguous allele combinations (i.e. A/T or G/C).