Which softwares do you suggest to analysis CNV with Human660W-Quad_v1_H sap array?

Question

[Peter]

I have paired tumor samples data from Human660W-Quad_v1_H sap array. I want to detect CNV based on these data. Which softwares do you suggest to analysis CNV with Human660W-Quad_v1_H sap array?

Answer 1

[bernatgel]

We have been using ASCAT with Illumina SNP-array data and we are quite happy with it, although in recent times we have been using also GAP. GAP is really painful to use (it's not a package per se but a series of scripts with quite a few hardcoded paths and filenames... but if you get to make it work it can give you very good results. Our experience is with very altered and aneuploid tumors with some stromal "contamination", maybe other tools would be better if you expect to find just a handful of alterations per tumor.