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, 12:35, 22 June 2015
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| *GATK v3.1-1-g07a4bf8 | | *GATK v3.1-1-g07a4bf8 |
| *vt normalize v0.5 | | *vt normalize v0.5 |
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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? |
| + | * 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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| = Citation = | | = Citation = |