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Jump to navigationJump to search→Here is an example where this normalization algorithm fails
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. Thus before you convince yourself that a representation is incorrect, consider the following factors:
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.
When performing decomposition and construction, I think the following factors should be considered:
* Are your variants describing just a single individual or a population?
* Are the genotypes (if any) in your individual(s) phased?
Depending on the context, you will obtain different answers.
[https://github.com/atks/vt/issues/16 An example of inconsistent variant representation due to using vt normalize]
[https://github.com/atks/vt/issues/16 An example of inconsistent variant representation due to using vt normalize]
