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Targeted interrogation of copy number variation using SCIMMkit.

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

SUBMITTER: Zerr T

PROVIDER: S-EPMC2796813 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

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Targeted interrogation of copy number variation using SCIMMkit.

Zerr Troy T Cooper Gregory M GM Eichler Evan E EE Nickerson Deborah A DA

Bioinformatics (Oxford, England) 20091021 1

<h4>Summary</h4>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 a ...[more]

PMID: 19846438

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