Generate Parameters

Population parameter files can be retrieved from one of the pre-built templates with the following command. The templates are example parameters for your convenience and should be tailored to your population of interest where appropriate.

To learn more about what the parameters represent and how to optimize them for your analysis see the guide Tailoring Parameters.

Arguments

--generate_params [SPECIES]

Save a local copy of a population parameter file from a chosen species template in format GenSpe_Elementtype_Params.py.

Available species: selfing, aratha_cds, aratha_phastcons, dromel_cds, dromel_utr, dromel_phastcons, homsap_cds

--dir [path/to/NewParams.py]

Optional path to save parameters (defaults to ./SpeciesParams.py).

Example

Bvalcalc --generate_params homsap_cds

This will save a copy of HomSap_Cds_Params.py with population parameters specific to human CDS (coding sequence) in the current folder, ready for calculating B