Targeted interrogation of copy number variation using SCIMMkit

Bioinformatics. 2010 Jan 1;26(1):120-2. doi: 10.1093/bioinformatics/btp606. Epub 2009 Oct 21.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • DNA Mutational Analysis / methods*
  • Gene Dosage / genetics*
  • Gene Targeting / methods*
  • Genetic Variation / genetics*
  • Molecular Sequence Data
  • Polymorphism, Single Nucleotide / genetics*
  • Sequence Analysis, DNA / methods*
  • Software