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Advances in Bioinformatics
Volume 2011, Article ID 657341, 11 pages
Research Article

NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels

1Department of Crop and Animal Sciences, Humboldt-University of Berlin, Invalidenstraße 42, 10115 Berlin, Germany
2Faculty of Science and Technology, Free University of Bozen, Piazza Università 5, 39100 Bozen, Italy

Received 27 June 2011; Accepted 11 August 2011

Academic Editor: Huixiao Hong

Copyright © 2011 Jens Aßmus et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Typically, next-generation resequencing projects produce large lists of variants. NovelSNPer is a software tool that permits fast and efficient processing of such output lists. In a first step, NovelSNPer determines if a variant represents a known variant or a previously unknown variant. In a second step, each variant is classified into one of 15 SNP classes or 19 InDel classes. Beside the classes used by Ensembl, we introduce POTENTIAL_START_GAINED and START_LOST as new functional classes and present a classification scheme for InDels. NovelSNPer is based upon the gene structure information stored in Ensembl. It processes two million SNPs in six hours. The tool can be used online or downloaded.