SCIMMkit

Introduction

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.