Genotype¶

class hail.representation.Genotype(gt, ad=None, dp=None, gq=None, pl=None)[source]¶

An object that represents an individual’s genotype at a genomic locus.

Parameters:	gt (int or None) – Genotype hard call ad (list of int or None) – allelic depth (1 element per allele including reference) dp (int or None) – total depth gq (int or None) – genotype quality pl (list of int or None) – phred-scaled posterior genotype likelihoods (1 element per possible genotype)

Attributes

`ad`	Returns the allelic depth.
`dp`	Returns the total depth.
`gp`	Returns the linear-scaled genotype probabilities.
`gq`	Returns the phred-scaled genotype quality.
`gt`	Returns the hard genotype call.
`pl`	Returns the phred-scaled genotype posterior likelihoods.

Methods

`__init__`	Initialize a Genotype object.
`dosage`	Returns the expected value of the genotype based on genotype probabilities, \(\mathrm{P}(\mathrm{Het}) + 2 \mathrm{P}(\mathrm{HomVar})\).
`fraction_reads_ref`	Returns the fraction of reads that are reference reads.
`is_called`	True if the genotype call is non-missing.
`is_called_non_ref`	True if the genotype call contains any non-reference alleles.
`is_het`	True if the genotype call contains two different alleles.
`is_het_non_ref`	True if the genotype call contains two different alternate alleles.
`is_het_ref`	True if the genotype call contains one reference and one alternate allele.
`is_hom_ref`	True if the genotype call is 0/0
`is_hom_var`	True if the genotype call contains two identical alternate alleles.
`is_not_called`	True if the genotype call is missing.
`num_alt_alleles`	Returns the count of non-reference alleles.
`od`	Returns the difference between the total depth and the allelic depth sum.
`one_hot_alleles`	Returns a list containing the one-hot encoded representation of the called alleles.
`one_hot_genotype`	Returns a list containing the one-hot encoded representation of the genotype call.
`p_ab`	Returns the p-value associated with finding the given allele depth ratio.

ad¶

Returns the allelic depth.

Return type:	list of int or None

dosage()[source]¶

Returns the expected value of the genotype based on genotype probabilities, \(\mathrm{P}(\mathrm{Het}) + 2 \mathrm{P}(\mathrm{HomVar})\). Genotype must be bi-allelic.

Return type:	float

dp¶

Returns the total depth.

Return type:	int or None

fraction_reads_ref()[source]¶

Returns the fraction of reads that are reference reads.

Equivalent to:

>>> g.ad[0] / sum(g.ad)

Return type:	float or None

gp¶

Returns the linear-scaled genotype probabilities.

Return type:	list of float of None

gq¶

Returns the phred-scaled genotype quality.

Returns:	int or None

gt¶

Returns the hard genotype call.

Return type:	int or None

is_called()[source]¶

True if the genotype call is non-missing.

Return type:	bool

is_called_non_ref()[source]¶

True if the genotype call contains any non-reference alleles.

Return type:	bool

is_het()[source]¶

True if the genotype call contains two different alleles.

Return type:	bool

is_het_non_ref()[source]¶

True if the genotype call contains two different alternate alleles.

Return type:	bool

is_het_ref()[source]¶

True if the genotype call contains one reference and one alternate allele.

Return type:	bool

is_hom_ref()[source]¶

True if the genotype call is 0/0

Return type:	bool

is_hom_var()[source]¶

True if the genotype call contains two identical alternate alleles.

Return type:	bool

is_not_called()[source]¶

True if the genotype call is missing.

Return type:	bool

num_alt_alleles()[source]¶

Returns the count of non-reference alleles.

This function returns None if the genotype call is missing.

Return type:	int or None

od()[source]¶

Returns the difference between the total depth and the allelic depth sum.

Equivalent to:

g.dp - sum(g.ad)

Return type:	int or None

one_hot_alleles(num_alleles)[source]¶

Returns a list containing the one-hot encoded representation of the called alleles.

This one-hot representation is the positional sum of the one-hot encoding for each called allele. For a biallelic variant, the one-hot encoding for a reference allele is [1, 0] and the one-hot encoding for an alternate allele is [0, 1]. Thus, with the following variables:

num_alleles = 2
hom_ref = Genotype(0)
het = Genotype(1)
hom_var = Genotype(2)

All the below statements are true:

hom_ref.one_hot_alleles(num_alleles) == [2, 0]
het.one_hot_alleles(num_alleles) == [1, 1]
hom_var.one_hot_alleles(num_alleles) == [0, 2]

This function returns None if the genotype call is missing.

Parameters:	num_alleles (int) – number of possible alternate alleles
Return type:	list of int or None

one_hot_genotype(num_genotypes)[source]¶

Returns a list containing the one-hot encoded representation of the genotype call.

A one-hot encoding is a vector with one ‘1’ and many ‘0’ values, like [0, 0, 1, 0] or [1, 0, 0, 0]. This function is useful for transforming the genotype call (gt) into a one-hot encoded array. With the following variables:

num_genotypes = 3
hom_ref = Genotype(0)
het = Genotype(1)
hom_var = Genotype(2)

All the below statements are true:

hom_ref.one_hot_genotype(num_genotypes) == [1, 0, 0]
het.one_hot_genotype(num_genotypes) == [0, 1, 0]
hom_var.one_hot_genotype(num_genotypes) == [0, 0, 1]

This function returns None if the genotype call is missing.

Parameters:	num_genotypes (int) – number of possible genotypes
Return type:	list of int or None

p_ab(theta=0.5)[source]¶

Returns the p-value associated with finding the given allele depth ratio.

This function uses a one-tailed binomial test.

This function returns None if the allelic depth (ad) is missing.

Parameters:	theta (float) – null reference probability for binomial model
Return type:	float

pl¶

Returns the phred-scaled genotype posterior likelihoods.

Return type:	list of int or None