Variant Normalization - Revision history

Atks: /* Other versions */

2016-08-01T13:55:06Z

Other versions

← Older revision		Revision as of 13:55, 1 August 2016
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	[http://bioinformatics.oxfordjournals.org/content/31/13/2202 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.]		[http://bioinformatics.oxfordjournals.org/content/31/13/2202 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.]

	= ~~Other versions~~ =		= Translations =

	A mandarin translation can be found [http://www.lyon0804.com/fan-yi-variant-normalization.html here]		A mandarin translation can be found [http://www.lyon0804.com/fan-yi-variant-normalization.html here]

Atks: /* Citation */

2016-07-29T16:33:07Z

Citation

← Older revision		Revision as of 16:33, 29 July 2016
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	[http://bioinformatics.oxfordjournals.org/content/31/13/2202 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.]		[http://bioinformatics.oxfordjournals.org/content/31/13/2202 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.]

			= Other versions =

			A mandarin translation can be found [http://www.lyon0804.com/fan-yi-variant-normalization.html here]

	= Maintained by =		= Maintained by =

	This page is maintained by [mailto:atks@umich.edu Adrian].		This page is maintained by [mailto:atks@umich.edu Adrian].

Atks: /* Here is an example where this normalization algorithm fails */

2015-07-02T19:10:09Z

Here is an example where this normalization algorithm fails

← Older revision		Revision as of 19:10, 2 July 2015
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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~~]		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/suppl/2015/02/19/btv112.DC1/VtNormApplicationNote_supp_20141113_1346.pdf]

Atks: /* Citation */

2015-07-02T19:09:34Z

Citation

← Older revision		Revision as of 19:09, 2 July 2015
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	= Citation =		= Citation =

	[http://bioinformatics.oxfordjournals.org/content/~~early~~/~~2015~~/~~03/22/bioinformatics.btv112~~ Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.]		[http://bioinformatics.oxfordjournals.org/content/31/13/2202 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.]

	= Maintained by =		= Maintained by =

	This page is maintained by [mailto:atks@umich.edu Adrian].		This page is maintained by [mailto:atks@umich.edu Adrian].

Atks: /* Citation */

2015-06-22T16:35:27Z

Citation

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 *GATK v3.1-1-g07a4bf8
 *vt normalize v0.5
 = Citation =

Atks: /* Here is an example where this normalization algorithm fails */

2015-06-22T16:35:07Z

Here is an example where this normalization algorithm fails

← Older revision		Revision as of 16:35, 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.

	~~= Here is an example where this normalization algorithm fails =~~

	~~We distinguish the concepts of normalization and decomposition/reconstruction of variants as follows:~~


	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]


	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.


	~~If your example contains the decomposition or reconstruction of variants, then it is probable that you can find inconsistencies.~~


	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]~~

	= Implementation =		= Implementation =

Atks: /* Citation */

2015-05-07T12:16:58Z

Citation

← Older revision		Revision as of 12:16, 7 May 2015
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	= Citation =		= Citation =

	[http://bioinformatics.oxfordjournals.org/content/early/2015/03/22/bioinformatics.btv112 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics. ~~doi: 10.1093/bioinformatics/btv112~~ ]		[http://bioinformatics.oxfordjournals.org/content/early/2015/03/22/bioinformatics.btv112 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.]

	= Maintained by =		= Maintained by =

	This page is maintained by [mailto:atks@umich.edu Adrian].		This page is maintained by [mailto:atks@umich.edu Adrian].

Atks: /* Citation */

2015-05-07T12:16:42Z

Citation

← Older revision		Revision as of 12:16, 7 May 2015
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	= Citation =		= Citation =

	[http://bioinformatics.oxfordjournals.org/content/early/2015/02/19/bioinformatics.btv112~~.abstract?keytype=ref&ijkey=2kB1TkBGzkoP1gd~~ Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics. doi: 10.1093/bioinformatics/btv112 ]		[http://bioinformatics.oxfordjournals.org/content/early/2015/03/22/bioinformatics.btv112 Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics. doi: 10.1093/bioinformatics/btv112 ]

	= Maintained by =		= Maintained by =

	This page is maintained by [mailto:atks@umich.edu Adrian].		This page is maintained by [mailto:atks@umich.edu Adrian].

Atks: /* Here is an example where this normalization algorithm fails */

2015-03-28T21:25:08Z

Here is an example where this normalization algorithm fails

← Older revision		Revision as of 21:25, 28 March 2015
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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. ~~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.


	* Are your variants describing just a single individual?		When performing decomposition and construction, I think the following factors should be considered:
	* Are the ~~genotypes in your individual phased?~~
	* Are your variants representing a population of individuals?
	* Are you sure that your representation algorithm is unique in view of the above 3 points?

			* 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]

Atks: /* Here is an example where this normalization algorithm fails */

2015-03-28T21:15:38Z

Here is an example where this normalization algorithm fails

← Older revision		Revision as of 21:15, 28 March 2015
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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.		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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	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.		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:


			* Are your variants describing just a single individual?
			* Are the genotypes in your individual phased?
			* Are your variants representing a population of individuals?
			* Are you sure that your representation algorithm is unique in view of the above 3 points?