Call

class hail.genetics.Call

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

Parameters:

• alleles (list of int) – List of alleles that compose the call.

• phased (bool) – If True, the alleles are phased and the order is specified by alleles.

Note

This object refers to the Python value returned by taking or collecting Hail expressions, e.g. mt.GT.take(5`). This is rare; it is much more common to manipulate the CallExpression object, which is constructed using the following functions:

• call()

• unphased_diploid_gt_index_call()

• parse_call()

Attributes

alleles	Get the alleles of this call.
phased	True if the call is phased.
ploidy	The number of alleles for this call.

Methods

is_diploid	True if the ploidy == 2.
is_haploid	True if the ploidy == 1.
is_het	True if the call contains two different alleles.
is_het_non_ref	True if the call contains two different alternate alleles.
is_het_ref	True if the call contains one reference and one alternate allele.
is_hom_ref	True if the call has no alternate alleles.
is_hom_var	True if the call contains identical alternate alleles.
is_non_ref	True if the call contains any non-reference alleles.
n_alt_alleles	Returns the count of non-reference alleles.
one_hot_alleles	Returns a list containing the one-hot encoded representation of the called alleles.
unphased_diploid_gt_index	Return the genotype index for unphased, diploid calls.

property alleles

Get the alleles of this call.

Returns:

list of int

is_diploid()

True if the ploidy == 2.

Return type:

bool

is_haploid()

True if the ploidy == 1.

Return type:

bool

is_het()

True if the call contains two different alleles.

Return type:

bool

is_het_non_ref()

True if the call contains two different alternate alleles.

Return type:

bool

is_het_ref()

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

Return type:

bool

is_hom_ref()

True if the call has no alternate alleles.

Return type:

bool

is_hom_var()

True if the call contains identical alternate alleles.

Return type:

bool

is_non_ref()

True if the call contains any non-reference alleles.

Return type:

bool

n_alt_alleles()

Returns the count of non-reference alleles.

Return type:

int

one_hot_alleles(n_alleles)

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

Examples

>>> n_alleles = 2
>>> hom_ref = hl.Call([0, 0])
>>> het = hl.Call([0, 1])
>>> hom_var = hl.Call([1, 1])

>>> het.one_hot_alleles(n_alleles)
[1, 1]

>>> hom_var.one_hot_alleles(n_alleles)
[0, 2]

Notes

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].

Parameters:

n_alleles (int) – Number of total alleles, including the reference.

Returns:

list of int

property phased

True if the call is phased.

Returns:

bool

property ploidy

The number of alleles for this call.

Returns:

int

unphased_diploid_gt_index()

Return the genotype index for unphased, diploid calls.

Returns:

int