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This is implemented in [http://genome.sph.umich.edu/wiki/Vt#Normalization vt].
This is implemented in [http://genome.sph.umich.edu/wiki/Vt#Normalization vt].
== Algorithm for Normalization ==
So now that we know how to tell if a variant is normalized, we simply need to manipulate the variant till the rightmost ends of the alleles are not the same, apply truncation to the superfluous nucleotides on the left side of the variant to obtain a normalized variant.
The algorithm to normalize a variant; biallelic or multiallelic is as follows:
[[Image:variant_normalization_algorithm.png|none|600px|Lines 1 to 8 performs the left alignment and ensures parsimonious representation on the right side. Lines 9 to 11 ensures parsimonious representation on the left side. ]]
Lines 1 to 8 performs the left alignment and ensures parsimonious representation on the right side. Lines 9 to 11 ensures parsimonious representation on the left side.
== Why you should use the implementation of normalization in vt ==
== Why you should use the implementation of normalization in vt ==
