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Is there an easily implementable analysis (R based) for copy number, ROH, mosaicism, and ploidy in R using Illumina 850K SNP array data?

I already use karyostudio and genome studio but am curious if there are some R based packages can offer some better ways to visualize the data. Are there R-based packages that could be used for internal database formation i.e. curation of variants observed?

illumina array omni snp 850k data

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