While reading the literature,it is not very clear to me the rationale of using one or the another.
http://genomebiology.com/2011/12/4/R41
http://www.nature.com/nbt/journal/v30/n5/full/nbt.2203.html
In my opinion, GISTICs primary goal is to identify genes affected by focal CNAs while Absolute is used to infer clonal composition of tumor samples.
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