Structural Variations (SVs) and Copy Number Variations (CNVs) are a major source of genomic variation. However, compared to SNPs, accurate detection, genotyping and understanding of CNVs is lagging behind due to much greater analytical challenges related to SV/CNV detection and analysis. In our lab we analyse SVs/CNVs using high-throughput sequencing and different analytical approaches. Related tools, databases and publications are listed below.

Tools Papers
vcf2diploid personal genome constructor, it can be used to construct a personal diploid genome sequence by including personal variants into reference genome. 2011
CNVnator a tool for CNV discovery and genotyping from depth of read mapping. 2011a,2011b
AGE a tools that implements an algorithm for optimal alignment of sequences with SVs. 2011
BreakSeq a pipeline for annotation, classification and analysis of SVs at single nucleotide resolution. 2010
PEMer a computational and simulation framework for discovering SVs by paired-end read mapping. 2009,2007
Databases and Datasets Papers
BreakSeq The database contains information about breakpoints of SVs at single nucleotide level. The information has been gathered from literature. 2010
Break-DB The database contains information about SVs and associated breakpoints detected by PEMer. 2009
Web supplements
Supplement to Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
Nat Biotechnol. 2010 Jan;28(1):47-55. Epub 2009 Dec 27.
Supplement to Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome.
Science. 2007 Oct 19;318(5849):420-6. Epub 2007 Sep 27.
Click here for a complete list of SV-related papers published in our group. Individual references to some of these have also been provided above.