I have (human) Illumina genome wide SNP array copy number data. For each SNP genomewide, I have Log R Ratio (LRR) and B Allele Frequency (BAF).
What tool(s) can I use to get the integer copy numbers (either -3 to +3 or 0 to inf) for each cytoband and for each gene in the genome?
I assume that people routinely do this? Are there any R packages/pipelines/code to do this?
Do people use
GISTIC for this?