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Variant Normalization (view source)

Revision as of 17:58, 20 May 2014

784 bytes removed ,  17:58, 20 May 2014
→‎Algorithm for Normalization
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:&rArr; A variant is normalized if and only if it is has no superfluous nucleotides on the left side and right parsimonious and left aligned.  (definition of left parsimony) <br>
 
:&rArr; A variant is normalized if and only if it is has no superfluous nucleotides on the left side and right parsimonious and left aligned.  (definition of left parsimony) <br>
 
:&rArr; A variant is normalized if and only if it is has no superfluous nucleotides on the left side and each allele do not end with the same type of nucleotide. (lemma 1) <br>
 
:&rArr; A variant is normalized if and only if it is has no superfluous nucleotides on the left side and each allele do not end with the same type of nucleotide. (lemma 1) <br>
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= Algorithm for Normalization =
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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.
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The algorithm to normalize a variant; biallelic or multiallelic is as follows:
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[[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. ]]
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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.
      
= Implementation =
 
= Implementation =
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/10441"

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