RT Journal Article
SR Electronic
T1 Improving the Power of Structural Variation Detection by Augmenting the Reference
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 019109
DO 10.1101/019109
A1 Jan Schröder
A1 Santhosh Girirajan
A1 Anthony T. Papenfuss
A1 Paul Medvedev
YR 2015
UL http://biorxiv.org/content/early/2015/05/08/019109.abstract
AB The uses of the Genome Reference Consortium’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.