Tools For Analyzing Copy Number Variation On All-Tumor Exome-Seq Samples

Question

[newDNASeqer]

My exome-seq data all derived from sequencing tumor samples. I am wondering what's the best tool for detecting CNVs in these samples. From my understanding, most CNV tools rely on the changes in depth of coverage to call CNVs. Is there any tool you recommend?

I've also taken a look at VarScan, is it only applicable to normal/tumor sample pair?

Answer 1

[brentp]

You can use cn.mops: http://www.bioconductor.org/packages/release/bioc/html/cn.mops.html to get copy-number estimates in your samples.

It obviously won't tell you if they are different from normal, but maybe you can overlap with existing, known CNVs.

You could also look for regions with a consistently high copy-number across your samples and see if / how they are related to the cancer you're studying.

Answer 2

[Ryan D]

A group here has had a great deal of success in using Varscan2 and ExomCNV due to the non-uniform nature of exon coverage across the genome. See the paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759720/ , though XHMM has worked fairly well for us if you have a number of samples run under the same sequencing parameters. I might recommend the former.