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