Targeted interrogation of copy number variation using SCIMMkit.
CONCLUSIONS
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.


BACKGROUND
Source code and documentation are available for noncommercial use at http://droog.gs.washington.edu/scimmkit.
Zerr
Troy
T
Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. troyz@u.washington.edu
Cooper
Gregory M
GM
Eichler
Evan E
EE
Nickerson
Deborah A
DA
D000465:Algorithms; D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D018628:Gene Dosage / Q000235:genetics*; D018390:Gene Targeting / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software