I was working for 5 years with NGS data and CNV detection, but now I have to perform CNV calling in .CEL files from Affymetrix v6 arrays. At first, I have no idea how to operate with such files (should I download some converter to vcf or txt or other format?). At second, I need to perform tumor CNA calling there (of course I have tumor-normal data). Which tool is the best, taking into account purity and clonality of samples?
Thanks a lot for any hints!
(of course I googled for papers, but I am a complete newbie in this field and a bit overwhelmed, everybody says 'oh we are the best buy our software', but somehow I dont trust most of them and also I work in academia and looking for something which is free for research)