alphagenome.interpretation.ism.ism_variants

alphagenome.interpretation.ism.ism_variants(interval, sequence, vocabulary='ACGT', skip_n=False)

Create a list of all possible single nucleotide variants for an interval.

Parameters:

• interval (Interval) – Interval for which to generate the variants.

• sequence (str) – Sequence extracted from the reference genome at the interval. Needs to have the same length as interval.width.

• vocabulary (str (default: 'ACGT')) – Vocabulary of possible alternative bases contained in sequence.

• skip_n (bool (default: False)) – If True, skip the N bases.

Return type:

list[Variant]

Returns:

List of all possible single nucleotide variants for a genomic interval.