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Bioinformatics. 2017 Apr 1;33(7):1083-1085. doi: 10.1093/bioinformatics/btw789.

SVScore: an impact prediction tool for structural variation.

Author information

1
McDonnell Genome Institute.
2
Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.

Abstract

Summary:

Here we present SVScore, a tool for in silico structural variation (SV) impact prediction. SVScore aggregates per-base single nucleotide polymorphism (SNP) pathogenicity scores across relevant genomic intervals for each SV in a manner that considers variant type, gene features and positional uncertainty. We show that the allele frequency spectrum of high-scoring SVs is strongly skewed toward lower frequencies, suggesting that they are under purifying selection, and that SVScore identifies deleterious variants more effectively than alternative methods. Notably, our results also suggest that duplications are under surprisingly strong selection relative to deletions, and that there are a similar number of strongly pathogenic SVs and SNPs in the human population.

Availability and Implementation:

SVScore is implemented in Perl and available freely at {{ http://www.github.com/lganel/SVScore }} for use under the MIT license.

Contact:

ihall@wustl.edu.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28031184
PMCID:
PMC5408916
DOI:
10.1093/bioinformatics/btw789
[Indexed for MEDLINE]
Free PMC Article

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