ABOUT affymetrix genotyping console (GTC) software and TCGA CNV workflow
The TCGA CNV workflow uses Birdsuite to estimate raw copy number (CN). The affymetrix genotyping console (GTC) use similar algorithm developed by broad. Is GTC used to estimate raw CN, too?
Otherwise, could GTC output files that could be input files for DNAcopy package used by TCGA in the copy number segement stage.
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