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
... [Show full abstract] 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 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 4,751 SV from one sample of the 1000 Genomes Project, integrating the sample information of 4 million of SNV/indel, in less than 60 seconds.
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/.
Contact:
veronique.geoffroy@inserm.fr.
Supplementary information:
In order to provide a ready to start installation of AnnotSV, each annotation source (that do not require a commercial license) is already provided with the AnnotSV sources. Supplementary data are available at Bioinformatics online.