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Conditional and interaction analysis

In case you want to perform conditional or interaction analysis, you can configure the following parameters:

  • interaction_cov: run GxE test specifying the interacting covariate from covariate table. For GxE tests where the interacting variable is categorical, you can specify the baseline level using 'VARNAME[BASE_LEVEL]' (e.g. 'BMI[<25]'). Otherwise, the first value found in the covariate file will be used as the baseline level.

  • interaction_snp: run GxG test specifying the interacting variant ID For GxG tests, the default coding for the interacting variant is additive. If you would like to use dominant/recessive/categorical coding, use 'SNP_NAME[dom/rec/cat]' (for example with dominant coding, 'SNPNAME[dom]' will allow for separate effects between carriers vs non-carriers of the interacting variant). The allowed values in the brackets are add/dom/rec/cat.

  • condition_list: run conditional analysis specifying a file with variant IDs to condition on

Note that to perform conditional/interaction analysis, an additional genotype dataset must be provided containing the SNP(s) used for conditioning/interaction. This can be configured using the following parameters:

  • additional_geno_format: can be bgen, pgen or bed.
  • additional_geno_file: prefix of the genotype dataset containing vars in condition_list or interaction var. This is mandatory for conditional or interaction analysis. Depending on the value of additional_geno_format, the pipeline expects specific files to be present
  • bgen: additional_geno_file.bgen, additional_geno_file.bgen.bgi, additional_geno_file.sample
  • bed: additional_geno_file.bed, additional_geno_file.bim, additional_geno_file.fam
  • pgen: additional_geno_file.pgen, additional_geno_file.psam, additional_geno_file.pvar