Journal Article

Targeted interrogation of copy number variation using SCIMMkit

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

in Bioinformatics

Volume 26, issue 1, pages 120-122
Published in print January 2010 | ISSN: 1367-4803
Published online October 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp606

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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 (SNP-Conditional Mixture Modeling), SCIMM-Search and SCOUT (SNP-Conditional OUTlier detection)] 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, efficiency and flexibility in experimental design.

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

Contact: troyz@u.washington.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1806 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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