sgkit.infer_sample_ploidy

sgkit.infer_sample_ploidy(ds, *, call_genotype='call_genotype', call_ploidy='call_ploidy', merge=True)

Infer the ploidy of each sample across all variants based on the number of fill (non-allele) values in call genotypes.

Parameters

ds : Dataset

Dataset containing genotype calls.

call_genotype : Hashable (default: 'call_genotype')

Input variable name holding call_genotype as defined by sgkit.variables.call_genotype_spec. Must be present in ds.

call_ploidy : Hashable (default: 'call_ploidy')

Input variable name holding call_ploidy as defined by sgkit.variables.call_ploidy_spec. If the variable is not present in ds, it will be computed using infer_call_ploidy().

merge : bool (default: True)

If True (the default), merge the input dataset and the computed output variables into a single dataset, otherwise return only the computed output variables. See Dataset merge behavior for more details.

Return type

Dataset

Returns

A dataset containing sgkit.variables.sample_ploidy_spec.