PT  - JOURNAL ARTICLE
AU  - Jan Schröder
AU  - Santhosh Girirajan
AU  - Anthony T. Papenfuss
AU  - Paul Medvedev
TI  - Improving the Power of Structural Variation Detection by Augmenting the Reference
AID  - 10.1101/019109
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 019109
4099  - http://biorxiv.org/content/early/2015/05/08/019109.short
4100  - http://biorxiv.org/content/early/2015/05/08/019109.full
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.