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  • SCIMMkit


    SCIMMkit is an integrated toolkit for targeted CNV detection and genotyping using Illumina Infinium II and GoldenGate BeadXpress assays. Three tools are provided:

  • SCIMM (Snp-Conditional Mixture Modeling), for genotyping polymorphic deletions

  • SCIMM-Search, for automatically generating probe sets to be used by SCIMM

  • SCOUT (Snp-Conditional Outlier detection), for detecting rare deletion and duplication variants

    Each of these tools analyzes a predefined set of probes within each targeted region, using a statistical model of observed fluorescence data which contains, for each SNP, separate location parameters for each homozygous allelic state (e.g. 'A/A', 'A/-' 'B/B', 'B/-') and a single dispersion parameter shared by all homozygous allelic states.

    Copyright (C) 2009 Deborah Nickerson and Troy Zerr