Variant

class alphagenome.data.genome.Variant(chromosome, position, reference_bases, alternate_bases, name='', info=<factory>)

Represents a genomic variant/mutation.

Differs from the Variant definition in a VCF file, which allows for multiple alternative bases and contains sample information. This Variant class does not include sample information or variant call quality information.

chromosome

The chromosome name (e.g., ‘chr1’, ‘1’).

position

The 1-based position of the variant on the chromosome.

reference_bases

The reference base(s) at the variant position. Most frequently (not always!), these correspond to the sequence in the reference genome at positions: [position, …, position + len(reference_bases) - 1]

alternate_bases

The alternate base(s) that replace the reference. For example, if sequence=’ACT’, position=2, reference_bases=’C’, alternate_bases=’TG’, then the actual (alternate) sequence would be ATGT.

name

An optional name for the variant (e.g., a dbSNP ID like rs206437).

info

An optional dictionary for additional variant information.

start

The 0-based start position of the variant (position - 1).

end

The 0-based end position (start + len(reference_bases)).

reference_interval

Reference genomic Interval spanned by the variant.

is_snv

True if single-nucleotide variant (len == 1 for ref and alt).

is_deletion

True if deletion (len(reference_bases) > len(alternate_bases)).

is_insertion

True if insertion (len(reference_bases) < len(alternate_bases)).

is_frameshift

True if indel length is not a multiple of 3.

is_indel

True if insertion or deletion.

is_structural

True if indel length is at least 50 bp.

Methods

alternate_overlaps(interval)	Checks if the variant's alternate overlaps with the interval.
as_truncated_str([max_length])	Truncates the variant str's ref and alt bases to the given max length.
copy()	Returns a deep copy of the variant.
from_dict(dictionary)	Creates a Variant from a dictionary.
from_str(string[, variant_format])	Creates a Variant from a string representation.
reference_overlaps(interval)	Checks if the variant's reference overlaps with the interval.
split(anchor)	Splits the variant into two at the anchor point.
to_dict()	Converts the variant to a dictionary.