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Bioinformatics Advance Access published online on October 21, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp606
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Targeted Interrogation of Copy Number Variation using SCIMMkit

Troy Zerr 1,*, Gregory M. Cooper 1, Evan E. Eichler 1,2 and Deborah A. Nickerson 1

1Department of Genome Sciences, University of Washington, Seattle, Washington 98195
2Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195

*To whom correspondence should be addressed. Mr. Troy Zerr, E-mail: troyz{at}u.washington.edu


  Abstract

Summary: Copy-number variants (CNVs) contribute substantially to human genomic diversity, and development of accurate and efficient methods for CNV genotyping is a central problem in exploring human genotype-phenotype associations. SCIMMkit provides a robust, integrated implementation of three previously validated algorithms (SCIMM, SCIMM-Search, and SCOUT) for targeted interrogation of CNVs using Illumina Infinium II and GoldenGate SNP assays. SCIMMkit is applicable to standardized genome-wide SNP arrays and customized multiplexed SNP panels, providing economy, effi-ciency, and flexibility in experimental design.

Availability: Source code and documentation are available for noncommercial use at http://droog.gs.washington.edu/scimmkit.

Contact: troyz{at}u.washington.edu

Supplementary Information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Martin Bishop

Received on August 14, 2009; revised on September 30, 2009; accepted on October 16, 2009

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