Improving the power of structural variation detection by augmenting the reference

Jan Schröder, Santhosh Girirajan, Anthony T. Papenfuss, Paul Medvedev

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)


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 systemfor 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 polymorphismin a population.

Original languageEnglish
Article numbere0136771
Number of pages10
JournalPLoS ONE
Issue number8
Publication statusPublished - 31 Aug 2015
Externally publishedYes

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