Question: Tools For Analyzing Copy Number Variation On All-Tumor Exome-Seq Samples
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gravatar for newDNASeqer
5.0 years ago by
newDNASeqer630
United States
newDNASeqer630 wrote:

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?

exome cnv • 3.2k views
ADD COMMENTlink modified 5.0 years ago by Ryan D3.3k • written 5.0 years ago by newDNASeqer630
0
gravatar for brentp
5.0 years ago by
brentp22k
Salt Lake City, UT
brentp22k wrote:

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.

ADD COMMENTlink written 5.0 years ago by brentp22k
0
gravatar for Ryan D
5.0 years ago by
Ryan D3.3k
USA
Ryan D3.3k wrote:

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.

ADD COMMENTlink written 5.0 years ago by Ryan D3.3k
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