varona.maf

Minor allele frequency (MAF) calculation.

This module provides a few competing strategies for obtaining MAF data from a VFC file.

class MafMethod(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: CiStrEnum

Enum for the MAF calculation method.

Values:

Value	Description
FR	Use the FR field in the info section of the variant to calculate the MAF.
BCFTOOLS	Only available if non-pysam bcftools is installed. Use the MAF field in the info section of the variant to calculate the MAF, which is added by bcftools +fill-tags.
SAMPLES	Description of SAMPLES method

Note: The BCFTOOLS value is conditionally available based on the presence of non-pysam bcftools.

maf_from_samples(variant: VariantRecord) → float

Compute the MAF from the sample genotypes in a variant.

This function assumes that the genotypes are in the “GT” key of the samples section of the variant.

Parameters:

variant – A pysam.VariantRecord object.

Returns:

The MAF value.

Raises:

KeyError if the “GT” key is not found in the samples section.

maf_from_fr(variant: VariantRecord) → float

Compute the MAF from the “FR” info value in a variant.

Parameters:

variant – A pysam.VariantRecord object.

Returns:

The MAF value derived from the “FR” info value.

Raises:

KeyError if the “FR” key is not found in the info section.

maf_from_bcftools(variant: VariantRecord) → float

Extract the “MAF” value from the info section in a variant.

This function assumes the presence of an “MAF” key in the info section. bcftools, if installed, may be used to add this key to the VCF file using a command like bcftools +fill-tags.

Parameters:

variant – A pysam.VariantRecord object.

Returns:

The MAF value.

Raises:

KeyError if the “MAF” key is not found in the info section.

maf_from_method(variant: VariantRecord, method: MafMethod) → float

A dispatcher for maf_from_fr(), maf_from_bcftools(), and maf_from_samples().

Parameters:

• variant – A pysam.VariantRecord object.

• method – The MAF calculation method.

Returns:

The MAF value.

Raises:

KeyError if the method is not recognized.