To my knowledge, Sequenza output files are tab-delimited text files, thus suitable for most software such as Annovar, wannovar, perhaps Variant Effect Predictor of ensemble.

Hi Bruno Batista Souza

CNV are hard to handle since you won't know the impact of loss (heterozygous) or gain on cell metabolism and special on transcriptome of the implicated genes. you can of course list the implicated genes (and their roles in pathways) and see if the CNV are overrepresented in one group against the other.

fred

Thanks Iman and Frederic for your supports... As Iman said, as sequenza output is tab delimited, I have used R to make a bed file with appropriate informations and now I'm gonna try AnnotSV to perform annotations. Frederic, you're right about everything, but I'm my case (I forgot to add this information) I'm looking for CNVs in a on target cancer pannel, so I'm going to be comparing two groups of pacientes, just like you said.

Great, if you can use R your choices are not limited to online tools, you'd find plenty of R packages for your purpose. Good luck.