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Workshop: Characterization of structural variants with next generation DNA sequencing

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4 Author(s)
Benjamin Raphael ; Brown University, Providence, RI, USA ; Suzanne Sindi ; Anna Ritz ; Ali Bashir

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 .

Published in:

Computational Advances in Bio and Medical Sciences (ICCABS), 2011 IEEE 1st International Conference on

Date of Conference:

3-5 Feb. 2011