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. 2015 Jul 1;31(13):2202-4.
doi: 10.1093/bioinformatics/btv112. Epub 2015 Feb 19.

Unified representation of genetic variants

Adrian Tan  1 , Gonçalo R Abecasis  1 , Hyun Min Kang  1
Affiliations

Unified representation of genetic variants

Adrian Tan et al. Bioinformatics. .

Abstract

A genetic variant can be represented in the Variant Call Format (VCF) in multiple different ways. Inconsistent representation of variants between variant callers and analyses will magnify discrepancies between them and complicate variant filtering and duplicate removal. We present a software tool vt normalize that normalizes representation of genetic variants in the VCF. We formally define variant normalization as the consistent representation of genetic variants in an unambiguous and concise way and derive a simple general algorithm to enforce it. We demonstrate the inconsistent representation of variants across existing sequence analysis tools and show that our tool facilitates integration of diverse variant types and call sets.

Availability and implementation: The source code is available for download at http://github.com/atks/vt. More detailed documentation is available at http://genome.sph.umich.edu/wiki/Variant_Normalization.

Contact: hmkang@umich.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Example of VCF entries representing the same variant. Left panel aligns each allele to the reference genome, and the right panel represents the variant in VCF. (A) is not left-aligned (B) is neither left-aligned nor parsimonious, (C) is not parsimonious and (D) is normalized
See this image and copyright information in PMC

References

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Publication types