I'm looking for a software tool to call copy number variations (CNV's) from NGS exome sequence data. There seem to be many possibilities (CNVnator, ExomeCNV, cn.MOPS, control-FREEC, BreakDancer.... etc.) Has anyone compared or evaluated any of these tools? Any recommendations for something that's easy to use, speedy, and accurate?
Read this
http://www.nature.com/nbt/journal/v30/n7/full/nbt.2311.html
CREST will be more useful and accurate compared to BreakDancer. Read this web-link for CREST (http://www.nature.com/nmeth/journal/v8/n8/full/nmeth.1628.html)
Some CNV tools used commonly are BreakDancer, Pindel, SVDetect, CNVDetect, PnvCNV
Thanks for these ideas everyone. Do you know if anyone's done a thorough comparison? There are so many that it's hard to what the pros and cons of each are.
I would start by looking at Galaxy, and see which tools have been integrated there - the best ones probably have.
You can also give VarScan2 a try, the link below is for the publication describing its performances
http://www.ncbi.nlm.nih.gov/pubmed/22300766
Lingyang et al, 2013 has done very nice comparative study. I would suggest to have a look at http://www.mdpi.com/2076-3905/2/3/171
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