Variant

class hail.representation.Variant(contig, start, ref, alts)

An object that represents a genomic polymorphism.

Parameters:

• contig (str or int) – chromosome identifier
• start (int) – chromosomal position (1-based)
• ref (str) – reference allele
• alts (str or list of str) – single alternate allele, or list of alternate alleles

Attributes

alt_alleles	List of alternate allele objects in this polymorphism.
contig	Chromosome identifier.
ref	Reference allele at this locus.
start	Chromosomal position (1-based).

Methods

__init__	x.__init__(…) initializes x; see help(type(x)) for signature
allele	Returns the string allele representation for the ith allele.
alt	Returns the alternate allele string, assumes biallelic.
alt_allele	Returns the alternate allele object, assumes biallelic.
in_X_PAR	True of this polymorphism is found on the pseudoautosomal region of chromosome X.
in_X_non_PAR	True of this polymorphism is found on the non-pseudoautosomal region of chromosome X.
in_Y_PAR	True of this polymorphism is found on the pseudoautosomal region of chromosome Y.
in_Y_non_PAR	True of this polymorphism is found on the non-pseudoautosomal region of chromosome Y.
is_autosomal	True if this polymorphism is located on an autosome.
is_autosomal_or_pseudoautosomal	True if this polymorphism is found on an autosome, or the PAR on X or Y.
is_biallelic	True if there is only one alternate allele in this polymorphism.
is_mitochondrial	True if this polymorphism is mapped to mitochondrial DNA.
locus	Returns the locus object for this polymorphism.
num_alleles	Returns the number of total alleles in this polymorphism, including the reference.
num_alt_alleles	Returns the number of alternate alleles in this polymorphism.
num_genotypes	Returns the total number of unique genotypes possible for this variant.
parse	Parses a variant object from a string.

allele(i)

Returns the string allele representation for the ith allele.

The reference is included in the allele index. The index of the first alternate allele is 1. The following is true for all variants:

>>> v_multiallelic.ref == v_multiallelic.allele(0)

Additionally, the following is true for all biallelic variants:

>>> v_biallelic.alt == v_biallelic.allele(1)

Parameters:i (int) – integer index of desired allele Returns:string representation of ith allele Return type:str

alt()

Returns the alternate allele string, assumes biallelic.

Fails if called on a multiallelic variant.

Return type:str

alt_allele()

Returns the alternate allele object, assumes biallelic.

Fails if called on a multiallelic variant.

Return type:AltAllele

alt_alleles

List of alternate allele objects in this polymorphism.

Return type:list of AltAllele

contig

Chromosome identifier.

Return type:str

in_X_PAR()

True of this polymorphism is found on the pseudoautosomal region of chromosome X.

Return type:bool

in_X_non_PAR()

True of this polymorphism is found on the non-pseudoautosomal region of chromosome X.

Return type:bool

in_Y_PAR()

True of this polymorphism is found on the pseudoautosomal region of chromosome Y.

Return type:bool

in_Y_non_PAR()

True of this polymorphism is found on the non-pseudoautosomal region of chromosome Y.

Return type:bool

is_autosomal()

True if this polymorphism is located on an autosome.

Return type:bool

is_autosomal_or_pseudoautosomal()

True if this polymorphism is found on an autosome, or the PAR on X or Y.

Return type:bool

is_biallelic()

True if there is only one alternate allele in this polymorphism.

Return type:bool

is_mitochondrial()

True if this polymorphism is mapped to mitochondrial DNA.

Return type:bool

locus()

Returns the locus object for this polymorphism.

Return type:Locus

num_alleles()

Returns the number of total alleles in this polymorphism, including the reference.

Return type:int

num_alt_alleles()

Returns the number of alternate alleles in this polymorphism.

Return type:int

num_genotypes()

Returns the total number of unique genotypes possible for this variant.

For a biallelic variant, this value is 3: 0/0, 0/1, and 1/1.

For a triallelic variant, this value is 6: 0/0, 0/1, 1/1, 0/2, 1/2, 2/2.

For a variant with N alleles, this value is:

\[\frac{N * (N + 1)}{2}\]

Return type:int

static parse(string)

Parses a variant object from a string.

There are two acceptable formats: CHR:POS:REF:ALT, and CHR:POS:REF:ALT1,ALT2,…ALTN. Below is an example of each:

>>> v_biallelic = Variant.parse('16:20012:A:TT')
>>> v_multiallelic = Variant.parse('16:12311:T:C,TTT,A')

Return type:Variant

ref

Reference allele at this locus.

Return type:str

start

Chromosomal position (1-based).

Return type:int