Targeted interrogation of copy number variation using SCIMMkit

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.