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, 12:35, 22 June 2015
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| | Thus A and B have to be at the same position and have the same length and variant normalization is unique. | | Thus A and B have to be at the same position and have the same length and variant normalization is unique. |
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| − | = Here is an example where this normalization algorithm fails =
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| − | We distinguish the concepts of normalization and decomposition/reconstruction of variants as follows:
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| − | Normalization involves reducing representations of a variant to a canonical representation. Normalization can be applied to biallelic variants or multiallelic variants. The problem of normalization is solvable and there exists a unique representation that is left aligned and parsimonious. Mathematical proof is published. [http://bioinformatics.oxfordjournals.org/content/early/2015/03/22/bioinformatics.btv112]
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| − | Decomposition of variants involves the breaking down of a variant record into multiple records. It may be done vertically - as in multiallelics becoming biallelics or it can be done horizontally - a cluster of indels and SNPs represented as a complex variant being splitted up into several records. Horizontal decompositions in general do not have a unique solution. Similarly, reconstruction combines several variant records into a single record and can be done vertically and horizontally too. Vertical decomposition of a multiallelic variant to a set of biallelic records is a many to one function. Construction of a set of biallelic variants into a multiallelic record is not unique as you need to considered all possible permutations of the haplotypes containing your alleles.
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| − | If your example contains the decomposition or reconstruction of variants, then it is probable that you can find inconsistencies.
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| − | It is important to distinguish the difference between normalization and decomposition/reconstruction. The notion of normalization implies that a variant can be reduced to a standardized form. If you were to include decomposition and reconstruction in your notion of normalization, you are bound to find inconsistencies simply due to the inherent issues of identifiability.
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| − | When performing decomposition and construction, I think the following factors should be considered:
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| − | * Are your variants describing just a single individual or a population?
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| − | * Are the genotypes (if any) in your individual(s) phased?
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| − | Depending on the context, you will obtain different answers.
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| − | [https://github.com/atks/vt/issues/16 An example of inconsistent variant representation due to using vt normalize]
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| | = Implementation = | | = Implementation = |
