CNV analysis from Illumina SNP array data
What are the best open source tools to analyse copy number variation from Illumina SNP array data? I am working with leukemia patient samples and I have illumina scan data from illumina infinium 850k cytoSNP beadchip array....the files are in IDAT/ GTC format.
I'm looking for open source tools ( preferably R based) to analyze CNV from these data.
Also if anybody has used iPsychCNV https://biopsyk.dk/ipsychcnv/ to analyze CNV calls, then what is the input file format ( example gtc /idat or any other format) that the software accepts?
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