@article {Schr{\"o}der019109, author = {Jan Schr{\"o}der and Santhosh Girirajan and Anthony T. Papenfuss and Paul Medvedev}, title = {Improving the Power of Structural Variation Detection by Augmenting the Reference}, elocation-id = {019109}, year = {2015}, doi = {10.1101/019109}, publisher = {Cold Spring Harbor Laboratory}, abstract = {The uses of the Genome Reference Consortium{\textquoteright}s human reference sequence can be roughly categorized into three related but distinct categories: as a representative species genome, as a coordinate system for identifying variants, and as an alignment reference for variation detection algorithms. However, the use of this reference sequence as simultaneously a representative species genome and as an alignment reference leads to unnecessary artifacts for structural variation detection algorithms and limits their accuracy. We show how decoupling these two references and developing a separate alignment reference can significantly improve the accuracy of structural variation detection, lead to improved genotyping of disease related genes, and decrease the cost of studying polymorphism in a population.}, URL = {https://www.biorxiv.org/content/early/2015/05/08/019109}, eprint = {https://www.biorxiv.org/content/early/2015/05/08/019109.full.pdf}, journal = {bioRxiv} }