Workshop: Characterization of structural variants with next generation DNA sequencing

Algorithms for structural variant identification from paired reads and from strobe reads are introduced. For paired reads, GASV+CC and GASV-Prob are designed. Each of these is built on the established Geometric Analysis of Structural Variants (GASV) program that precisely localizes the breakpoints of variants. GASV+CC combines read depth and paired reads analysis. GASV-Prob also includes paired reads with multiple possible alignments to the reference. The algorithms use a probability model to derive the likelihood of a structural variant. An algorithm for structural variation detection from strobe sequencing data is also presented. This algorithm formulates the problem of selecting an alignment for each subread of a strobe as an integer linear programming (ILP) problem, which was solve using standard approaches .