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Bioinformatics. 2018 Oct 15;34(20):3572-3574. doi: 10.1093/bioinformatics/bty304.

AnnotSV: an integrated tool for structural variations annotation.

Author information

1
Laboratoire de Génétique Médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine FMTS, Université de Strasbourg, Strasbourg, France.
2
Service de Génétique Médicale, CHU de Tours, Tours, France.
3
ICUBE UMR 7357, Complex Systems and Translational Bioinformatics (CSTB), Université de Strasbourg-CNRS-FMTS, Strasbourg, France.
4
Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg Cedex, France.
5
Institut de Génétique et de Biologie Moleculaire et Cellulaire, INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, France.
6
Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.

Abstract

Summary:

Structural Variations (SV) are a major source of variability in the human genome that shaped its actual structure during evolution. Moreover, many human diseases are caused by SV, highlighting the need to accurately detect those genomic events but also to annotate them and assist their biological interpretation. Therefore, we developed AnnotSV that compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to (i) interpret SV potential pathogenicity and (ii) filter out SV potential false positive. In particular, AnnotSV reports heterozygous and homozygous counts of single nucleotide variations (SNVs) and small insertions/deletions called within each SV for the analyzed patients, this genomic information being extremely useful to support or question the existence of an SV. We also report the computed allelic frequency relative to overlapping variants from DGV (MacDonald et al., 2014), that is especially powerful to filter out common SV. To delineate the strength of AnnotSV, we annotated the 4751 SV from one sample of the 1000 Genomes Project, integrating the sample information of four million of SNV/indel, in less than 60 s.

Availability and implementation:

AnnotSV is implemented in Tcl and runs in command line on all platforms. The source code is available under the GNU GPL license. Source code, README and Supplementary data are available at http://lbgi.fr/AnnotSV/.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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