Any Alternatives To Penncnv?

Question

[Biomed]

Hi, I have been using PennCNV-which probably is the most common tool for this purpose- for copy number detection on the Illumina 1M Duo chip data. I also found QuantiSNP on the web as a fairly established tool with a fairly good size user base. Do you know any alternative programs that I can use for CNV detection? What is the best practice in that? I am especially looking for your personal experiences and preferences. Thanks in advance

Answer 1

[Khader Shameer]

I am not sure if this is a best practice:

I have used cnvPartition for copy number variation analysis using Illumina chip. A detailed list of software from Illumina is available here . A related abstract from ASHG '08 evaluated seven different programs for CNV analysis. They report that cnvPartition and PennCNV showed better sensitivity in their comparative study.

Answer 2

[Katsubio]

Hi,

I've read a 2010 paper which compares 7 algorithms too, and it evaluates PennCNV as the worth, and QuantiSNP as the best ...

http://nar.oxfordjournals.org/content/38/9/e105.full

[Biomed]

Thanks a lot, this is a very nice review.

Answer 3

[Chris Miller]

There are lots of options. Off the top of my head, CBS, FaSEG, GLAD. (On preview, the abstract that Khader linked mentions seven different ones - start there).

Go ahead and compare them, but in the end, it's most important that you understand whichever algorithm you use. Each of them have different strengths and weaknesses, and may be suited to different types of data. The parameters you use will also matter. So pick one, learn it well, justify your choices, and then move on to more important downstream analysis.