Question: Whole Exome CNV tools
gravatar for BAGeno
15 months ago by
BAGeno170 wrote:


I want to ask that can we use breakerdancer, manta,delly, lumpy-sv for copy number variation calling of whole exome analysis? I have just whole exome data of five patients and I want to call their copy number variations.

sequencing cnv next-gen exome • 2.0k views
ADD COMMENTlink modified 15 months ago by ReWeeda70 • written 15 months ago by BAGeno170

Did you find a good tool to use? I have the same problem.

ADD REPLYlink written 7 months ago by gregorymcinnes10
gravatar for ReWeeda
15 months ago by
University of Bologna
ReWeeda70 wrote:

Hi BAGeno!

There are plenty of tools out there for CNVs detection from WES data! In addition to VarScan, cited by 2nelly, you can also try with:

I also suggest you to read this article.

I worked on CNVs detection in the recent past, and I developed a simple wrapper for a CNV simulator developed by NabaviLab that I found a little bit complicated in the first place. (WARNING : Simulation is slow!)

You can maybe simulate reads similar to you real data (similar depth of coverage, similar balancing in term of amplifications and deletions given what you expect to find, etc) with CNVs inserted in known place and then test the different tools to find which one suits better your task!

Hope this helps!

ADD COMMENTlink written 15 months ago by ReWeeda70

Hi ReWeeda,

I've used FREEC and CNVkit to analyze CNV profile fro WES tumor samples. In both cases the output profile looked noisy. Please see these links: 1) CNVkit problem: C: CNVKit noisy scatter plot 2) FREEC: CNV Profile figure

Please suggest something. Can I use CNVbencher for WES data? Thanks!

ADD REPLYlink modified 20 days ago • written 20 days ago by tanbiswas60
gravatar for 2nelly
15 months ago by
2nelly180 wrote:

Hi BAGeno,

I would suggest you to use VarScan, which is designed specifically for the type of data you have (WES).

Somatic Copy Number Alteration (CNA) Calling


ADD COMMENTlink written 15 months ago by 2nelly180

Thanks for your suggestion but VarScan is for tumor normal pair exome data. My patients are not cancer patients.

ADD REPLYlink written 15 months ago by BAGeno170
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