Required command line options¶

CHROM-START

Number of the chromosome to start the analysis at.

CHROM-END

Number of the chromosome to end the analysis at.

Note that analysis of a single chromosome can be run by specifying the same number for CHROM-START and CHROM-STOP. In fact, this is the way to run analysis for the X or Y chromosome

METHOD

Which regression method to use, can be one of linear, logistic, or coxph.

COHORT

The name of the cohort as defined in the /etc/probabel_config.cfg file. Using the cohort identifier from the config file the three actual ProbABEL binaries know where to find the genotypic information files (dosage files and/or probability files).

MODEL

The genetic model to be used. Can be either --additive for the additive model (requires genotype data in dosage form), or --allmodels to run all genetic models: additive, recessive, dominant, over-dominant and 2df.

PHENOTYPE

The name of the phenotype file, without its extension (which should be .PHE!).

Other options¶

Any options listed after the (mandatory) previous ones will be passed on to the underlying binary: palinear, palogist or pacoxph, depending on the METHOD.

The most commonly used option is the -o option, followed by a file name, this specifies the beginning of the file name for the output files.

Additional options¶

-h, --help Get additional help on how to run probabel. In this case none of the other options needs to be specified.