I have CytoscanHD array data of 20 pairs of cancer data(tumor/normal). Is there any efficient tools to analyze these data.How can I get the DNA copy number values and copy number segment. How could I calculate gene-level DNA segment score?
What are your data files? Do you have the intensities or only the ChAS report files.
If you have the intensities you can run a CNV caller for arrays like PennCNV. http://penncnv.openbioinformatics.org/en/latest/
After getting a list of CNVs and properly filtering them (segmental duplications are a must!), you can follow the plink rare CNV pipeline to analyze your data.