SVint, a light-weight tool for annotating structure variants located outside the coding genome

Jingqi Chen, Steven E. Brenner

We have developed SVint, a light-weight, easy to use tool for annotating the potential functional impact of structure variants (SVs). It has been challenging to estimate the impact of intergenic SVs, since they are located outside the coding genome. These SVs are frequently neglected during analysis of whole genome sequencing, despite evidence that large noncoding variants could disrupt enhancers and play an essential role in gene regulation. Functional annotation provided by SVint links SVs to regulatory elements and corresponding target genes. With this information, users can then further interpret the functional impact of the SVs. One innovation is that SVint uses the frequency that regulatory elements are disrupted by SVs to estimate the functional impact of SVs, rather than using the allele frequency of SVs--which relies on precise definition of SV boundaries. SVint can be useful in diagnostic whole genome sequencing analysis, especially for cases that cannot be solved through analysis of the protein coding regions.

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Contact: jingqi.chen@berkeley.edu