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Title:   Author  item
                                            Bickhart, Derekitem
                                            Cole, Johnitem
                                            Hutchison, Janaitem
                                            XU, LINGYANG - University Of Marylanditem
                                            Liu, Ge

                                                         - *George*
  Submitted to: World Congress of Genetics Applied in Livestock Production
                                    Publication Type: Proceedings
                                    Publication Acceptance Date: 4/21/2014
                                    Publication  Date: 8/17/2014
                                    Citation: Bickhart, D.M., Cole, J.B., Hutchison, J.L., Xu, L., Liu, G. 2014. Using the whole read: structural variant detection using NGS data. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 5 pp.Interpretive Summary:
                                Technical Abstract: Several classes of Structural Variants (SV) remain difficult to detect within sequenced genomes. Deletions and tandem duplications may affect a large proportion of variable genomic sequence space, yet their detection is still difficult to discern from false positive signals. Here, we present a method for detecting such variants from short-read sequence data using the orientation and distance of paired-end, and split-read mappings in addition to using read-depth as a filtering agent. We test our data using simulated SVs and find that our method is 27.5 times more precise than a competing detection program in detecting tandem duplications. Our method is also able to detect three times the number of deletions than the competition. This high degree of precision should enable better functional prediction of SVs from short-read sequence data.


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