Call

class hail.genetics.Call(alleles, phased=False)[source]

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.

Attributes

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

Methods

__init__ Initialize self.
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 two 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.
alleles

Get the alleles of this call.

Returns:list of int
is_diploid()[source]

True if the ploidy == 2.

Return type:bool
is_haploid()[source]

True if the ploidy == 1.

Return type:bool
is_het()[source]

True if the call contains two different alleles.

Return type:bool
is_het_non_ref()[source]

True if the call contains two different alternate alleles.

Return type:bool
is_het_ref()[source]

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

Return type:bool
is_hom_ref()[source]

True if the call has no alternate alleles.

Return type:bool
is_hom_var()[source]

True if the call contains two identical alternate alleles.

Return type:bool
is_non_ref()[source]

True if the call contains any non-reference alleles.

Return type:bool
n_alt_alleles()[source]

Returns the count of non-reference alleles.

Return type:int
one_hot_alleles(n_alleles)[source]

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
phased

True if the call is phased.

Returns:bool
ploidy

The number of alleles for this call.

Returns:int
unphased_diploid_gt_index()[source]

Return the genotype index for unphased, diploid calls.

Returns:int