normalize_variant

alphagenome.data.genome.normalize_variant(variant, extractor)

Normalize a Variant by left-aligning the reference and alternate bases.

Normalization applied following algorithm described in https://doi.org/10.1093/bioinformatics/btv112.

Parameters:

• variant (Variant) – The Variant to normalize.

• extractor (_FastaExtractorType) – The FastaExtractor to use for extracting the reference sequence.

Return type:

Variant

Returns:

The normalized Variant.