Table 1 List of commands available in the software and their corresponding usage description

-gf=

This specifies the genotype file. Typically .gen, .impute, .gen.gz.

-sf=

This specifies the sample file (.sample).

-t=

This specifies the time to event (column heading name) in the sample file.

-c=

This specifies the censoring indicator/outcome in the sample file.

-cov=

This specifies the covariates to adjust for in the model. Each one separated by a comma (,). Categorical factors need to be converted to binary as software only assumes continuous or binary covariates.

-lstart=

This specifies the line in the genotype file at which the start position of analysis will occur. Used to break large files into small batches for parallel computing.

-lstop=

This specifies the line in the genotype file at which the end position of analysis will occur. Typically the number of lines is equal to the number of SNPs in the file.

-sp=

The start position (in base pairs) on the chromosome. Still need to specify the number of lines in the file using -lstart & -lstop commands. <optional>

-ep=

The stop position (in base pairs) on the chromosome. <optional>

-chr=

This specifies the chromosome number to be output in the text file.

-p=

Enter “onlysnp” if only the results from the SNP analysis are to be output and “onlyint” if only the results from the SNP-covariate interaction analysis are to be output. <optional>

-m=

This specifies the choice of method for analysis. This is either “cox” for the Cox proportional hazards model or “weibull” for the parametric Weibull regression model.

-o=

This specifies the name of the file for output to be saved in. e.g., name.txt

-help

Outputs a full list of commands and usage help.