Bioinformatics. 2010 Jan 1;26(1):120-2. Epub 2009 Oct 21.

Targeted interrogation of copy number variation using SCIMMkit.

Zerr T, Cooper GM, Eichler EE, Nickerson DA.

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Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. troyz@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 (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.

PMID:: 19846438; [PubMed - indexed for MEDLINE]
PMCID:: PMC2796813

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Systematic assessment of copy number variant detection via genome-wide SNP genotyping. [Nat Genet. 2008]
Systematic assessment of copy number variant detection via genome-wide SNP genotyping.
Cooper GM, Zerr T, Kidd JM, Eichler EE, Nickerson DA. Nat Genet. 2008 Oct; 40(10):1199-203. Epub 2008 Sep 7.
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Cited by 1 PubMed Central article

CONAN: copy number variation analysis software for genome-wide association studies. [BMC Bioinformatics. 2010]
CONAN: copy number variation analysis software for genome-wide association studies.
Forer L, Schönherr S, Weissensteiner H, Haider F, Kluckner T, Gieger C, Wichmann HE, Specht G, Kronenberg F, Kloss-Brandstätter A. BMC Bioinformatics. 2010 Jun 14; 11:318. Epub 2010 Jun 14.

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