Improving the Power of Structural Variation Detection by Augmenting the Reference

Jan Schroeder; Santhosh Girirajan; Anthony T Papenfuss; Paul Medvedev

doi:10.1101/019109

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bioRxiv · 10.1101/019109

Improving the Power of Structural Variation Detection by Augmenting the Reference

Jan Schroeder·Santhosh Girirajan·Anthony T Papenfuss·Paul Medvedev

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Abstract

The uses of the Genome Reference Consortiums 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.

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Jan Schroeder, Santhosh Girirajan, Anthony T Papenfuss, Paul Medvedev. 2015-05-08. Improving the Power of Structural Variation Detection by Augmenting the Reference. https://doi.org/10.1101/019109

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