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CNVision
CNV prediction from Illumina genotyping data
... in Windows, however running the PennCNV component gives errors with the newer versions of PennCNV. CNVision was written to analyze data for the Simons Simplex Collection (SSC) autism data. A fill description of methods are given in the following paper which can be used to reference CNVision: http://www.ncbi.nlm.nih.gov/pubmed/21658581
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