Copy number variations from WES data

Hi,

I want to derive copy number variation information from whole exome data. Please suggest which tool/pipeline should I refer?

cnv wes

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updated 5.5 years ago by Rongxin •

• written 5.5 years ago by shivangi.agarwal800

Control-FREEC (shell)
DNAcopy (R)

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written 5.5 years ago by Kevin Blighe

I mostly use VarScan for this job. it is pretty straight forward and designed specifically for exome sequencing.

http://varscan.sourceforge.net/copy-number-calling.html

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written 5.5 years ago by 2nelly

1 answer

Hi,

Please see this paper Comparative study of whole exome sequencing-based copy number variation detection tools, which may provide you with some suggestions.

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written 5.5 years ago by Rongxin •

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