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Dear all,
any suggestions regarding a good algorithm to use to call CNV (copy number variants) in the cancer genomes ? many thanks !
-- bogdan
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We have been using whole-genome sequencing ;)
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FYI: you should rather post this as a comment as opposed to an answer.
Another question is whether or not you have matched normal samples?
In any event, there are a large number of tools listed on this seqanswers page that you can thumb through.
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Thank you Steve. Yes, we have normal-tumor pairs. I looked on the page you sent me the link to, and of course, also in the literature, there are many algorithms. I was just looking for an algorithm that most of the community trusts and the results have been verified. Thank you ;;)
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Using what technology? exome-seq? (still an "open" problem, AFIAK) whole genome sequencing? arrays?