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Jump to navigationJump to search→How to observe that a variant is not left aligned or parsimonious on the right side?
* If an Indel is left aligned and right parsimonious then each allele do not end with the same type of nucleotide.
* If an Indel is left aligned and right parsimonious then each allele do not end with the same type of nucleotide.
We first assume an indel is already left aligned and right parsimonious. Suppose all alleles have a length greater than 1, since the indel is right parsimonious, clearly, each allele do not end with the same type of nucleotide. Now, suppose that there exists an allele of length 1 and that all the alleles end with a particular nucleotide say 'A'. This is still considered right parsimonious as there are no superfluous nucleotides to remove without resulting in an empty allele. It is possible to extend all the alleles one position to the left by copying from a nucleotide on the reference genome, so now we have a superfluous nucleotide on the right side and can remove that nucleotide resulting in a new representation that shifts the Indel to the left by one position where one of the alleles is of length one. This is left aligning the Indel and thus there is a contradiction, so each allele cannot end with the same type of nucleotide.
We first assume an indel is already left aligned and right parsimonious. Suppose all alleles have a length greater than 1, since the indel is right parsimonious, clearly, each allele do not end with the same type of nucleotide. Now, suppose that there exists an allele of length 1 and that all the alleles end with a particular nucleotide say 'A'. This is still considered right parsimonious as there are no superfluous nucleotides to remove without resulting in an empty allele. It is possible to extend all the alleles one position to the left by copying from a nucleotide on the reference genome, so now we have a superfluous nucleotide on the right side and can remove that nucleotide resulting in a new representation that shifts the Indel to the left by one position where one of the alleles is of length one. This is left aligning the Indel and thus there is a contradiction, so each allele cannot end with the same type of nucleotide. This completes the proof.
= Algorithm for Normalization =
= Algorithm for Normalization =
